Glycoside hydrolases from thermophlic fungi

ABSTRACT

The present invention relates to isolated polypeptides having cellulolytic activity or hemicellulolytic activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is divisional application of U.S. application Ser. No.15/148,692 filed May 6, 2016, now U.S. Pat. No. 10,233,435, which isdivisional application of U.S. application Ser. No. 13/884,773 filedJan. 26, 2012, now U.S. Pat. No. 9,353,363, which is a 35 U.S.C. § 371national application of PCT/EP2012/051211 filed Jan. 26, 2012, whichclaims priority or the benefit under 35 U.S.C. § 119 of Europeanapplication no. 11152252.0 filed Jan. 26, 2011, the contents of whichare incorporated herein by reference.

REFERENCE TO A SEQUENCE LISTING

This application contains a Sequence Listing in computer readable form,which is incorporated herein by reference.

REFERENCE TO A COMPUTER PROGRAM LISTING APPENDIX

This application contains a Computer Program Listing Appendix containinga computer program submitted on duplicate compact discs, wherein theAppendix is incorporated herein by reference.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates to polypeptides having cellulolyticactivity or hemicellulolytic activity and polynucleotides encoding thepolypeptides. The present invention also relates to nucleic acidconstructs, vectors, and host cells comprising the polynucleotides aswell as methods of producing and using the polypeptides.

Description of the Related Art

There is a rising demand for more sustainable solutions to importantproblems of a modern society. Demand for more biological processes,products and solutions: Post peak oil era makes it inevitable that theglobal society at large will have to change from being based on carbonresources from fossils to using renewables. Renewable carbon resourcesare primarily made of plant materials. The conversion of plant materials(renewable carbon) to substitute the spectrum of useful and neededproducts (as energy, plastics, chemicals, etc.) obtained currently fromcrude oil is in general achieved by conversion of the plant biopolymersby the help of microbial enzymes/proteins. This need places high demandson discovery of enzymes and auxiliary proteins from microbes,sufficiently diverse and efficient for converting q wide spectrum ofdifferent types of biomass, available globally: from corn stover andwheat straw over sugar cane bagasse and empty flower bunches of oil palmto municipality waste and agroindustrial side streams.

The complexity of the biomass available places high demands to themicrobial products: Most agricultural products will have to be reservedfor feeding 9 billion people as well as for feeding animals for the foodchain. The biomass available for industrial purposes will largely in thefuture be crop residue/biowaste materials. Such materials are primarilycomposed of plant lignocelluloses, a highly recalcitrant structure whichneeds a host of enzymes for full decomposition. This requires evenhigher demands on the discovery of new and improved enzymes of microbialorigin.

An efficient way of enhancing the conversion rate of cellulosicfeedstock into ethanol is raising the temperature but this strategy islimited by the temperature stability of the available enzymes.

Another way of enhancing the conversion rate of cellulosic feedstockinto ethanol is to optimize the pretreatment of the feedstock beforeenzymatic degradation but this strategy is limited to acidicpretreatment methods by the pH optimum of the available enzymes.

A third way of enhancing the conversion rate of cellulosic feedstocksinto ethanol is adding polypeptides that enhance the cellulolyticactivity at low temperatures.

It would be advantageous in the art to improve the conversion ofcellulosic feedstock with polypeptides with cellulolytic activity athigh temperatures and to provide polypeptides with cellulolytic activitythat would be compatible with pretreatment at high pH values.Furthermore, it would be advantageous in the art to improve theconversion of cellulosic feedstocks with polypeptides with cellulolyticenhancing activity at high temperatures. However, only one polypeptidewith cellulolytic enhancing activity at high temperatures is known (U.S.Pat. No. 7,271,244). We have identified a number of thermophilic fungithat produce extracellular cellulase activity (endoglucanase andcellobiohydrolase activity) with higher thermostability than cellulaseactivity from other thermophilic fungi. In addition, several of thefungi produce cellulases that are highly active at pH values over 7. Asthe fungi produce cellulases with high thermostability and interestingpH optima it is reasonable to assume that other secreted enzymes fromthese fungi will also have higher thermostability and pH optima thannormally observed for fungal enzymes. Therefore, these fungi are usefulsources of new enzymes for industrial or other applications,

Protein and enzyme discovery can be based on genome sequencing (confinedto one organism at a time and depends on time consuming annotations),activity screening (requiring cloning and available high throughputassays), and searching for novelty through sequence similarity (e.g., aPCR based approach).

For decomposition of cellulose and hemicelluloses it is rather simple toconstruct suitable PCR primers for discovering novel xylanases (e.g.,GH10 and GH11) and novel endoglucanases (e.g., GH45) by PCR basedscreening. The 3D protein structure has through evolution maintainedlonger stretches of rather highly conserved regions, suitable for primerconstruction. However, other needed types of enzymes for cellulosedecomposition such as the cellobiohydrolases or the auxiliary proteinsbelonging to GH61 group have either very high sequence variation withineach protein family and/or limited areas of sufficient conservation orsequence similarity.

The motivation for the present invention is for more efficient PCR baseddiscovery. The basis is a belief that it should be possible to constructprimers based on further similarities than what is possible from analignment approach simply nested in the fact that it has been possibleto group enzymes and other proteins in protein families, which embraceproteins of even very low sequence similarity but with importantsimilarities in fold and characteristics/activities. Similarly, such isalso based on the fact that an in silico Blast search could identify aseries of proteins which are only distantly related sequence wise butsharing characteristics as, for example, grouping in the same proteinfamily (Henrissat B., 1991, A classification of glycosyl hydrolasesbased on amino-acid sequence similarities, Biochem. J. 280: 309-316, andHenrissat and Bairoch, 1996, Updating the sequence-based classificationof glycosyl hydrolases, Biochem. J. 316: 695-696).

Our hypothesis was that such possible regions suitable for primerconstruction could be identified based on bringing forward an advancedlevel of pattern recognition. This approach resulted in a method withsimplicity on the one hand and on the other hand significant valuableadvantages, such as speed.

The present invention provides polypeptides having cellulolytic activityor hemicellulolytic activity and polynucleotides encoding thepolypeptides.

SUMMARY OF THE INVENTION

The present invention relates to isolated polypeptides havingcellobiohydrolase activity selected from the group consisting of:

-   -   (a) a polypeptide having at least 80% sequence identity to the        polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4; at least 90%        sequence identity to the polypeptide of SEQ ID NO: 6; at least        91% sequence identity to the polypeptide of SEQ ID NO: 8; or at        least 99% sequence identity to the polypeptide of SEQ ID NO: 10;    -   (b) a polypeptide encoded by a polynucleotide that hybridizes        under at least very high stringency conditions with (i) the        polypeptide coding sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ        ID NO: 5, SEQ ID NO: 7, or SEQ ID NO: 9, (ii) the cDNA sequence        thereof, or (iii) the full-length complement of (i) or (ii);    -   (c) a polypeptide encoded by a polynucleotide having at least        80% sequence identity to the polypeptide coding sequence of SEQ        ID NO: 1 or SEQ ID NO: 3, or the cDNA sequences thereof; at        least 90% sequence identity to the polypeptide coding sequence        of SEQ ID NO: 5 or the cDNA sequence thereof; at least 91%        sequence identity to the polypeptide coding sequence of SEQ ID        NO: 7 or the cDNA sequences thereof; or at least 99% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 9 or        the cDNA sequence thereof;    -   (d) a variant comprising the polypeptide of SEQ ID NO: 2, SEQ ID        NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, or SEQ ID NO: 10 comprising a        substitution, deletion, and/or insertion at one or more (e.g.,        several) positions; and    -   (e) a fragment of the polypeptide of (a), (b), (c), or (d) that        has cellobiohydrolase activity.

The present invention relates to isolated polypeptides havingcellobiohydrolase activity selected from the group consisting of:

-   -   (a) a polypeptide having at least 70% sequence identity to the        polypeptide of SEQ ID NO: 12; at least 80% sequence identity to        the polypeptide of SEQ ID NO: 14 or SEQ ID NO: 16; at least 91%        sequence identity to the polypeptide of SEQ ID NO: 18; at least        96% sequence identity to the polypeptide of SEQ ID NO: 20; or at        least 98% sequence identity to the polypeptide of SEQ ID NO: 22        or SEQ ID NO: 24;    -   (b) a polypeptide encoded by a polynucleotide that hybridizes        under at least very high stringency conditions with (i) the        polypeptide coding sequence of SEQ ID NO: 11, SEQ ID NO: 13, SEQ        ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, or SEQ        ID NO: 23, (ii) the cDNA sequence thereof, or (iii) the        full-length complement of (i) or (ii);    -   (c) a polypeptide encoded by a polynucleotide having at least        70% sequence identity to the polypeptide coding sequence SEQ ID        NO: 11 or the cDNA sequence thereof; at least 80% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 13 or        SEQ ID NO: 15, or the cDNA sequences thereof; at least 91%        sequence identity to the polypeptide coding sequence of SEQ ID        NO: 17 or the cDNA sequence thereof; at least 96% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 19 or        the cDNA sequence thereof; or at least 98% sequence identity to        the polypeptide coding sequence of SEQ ID NO: 21 or SEQ ID NO:        23, or the cDNA sequences thereof;    -   (d) a variant comprising the polypeptide of SEQ ID NO: 12, SEQ        ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID        NO: 22, or SEQ ID NO: 24 comprising a substitution, deletion,        and/or insertion at one or more (e.g., several) positions;        and (e) a fragment of the polypeptide of (a), (b), (c), or (d)        that has cellobiohydrolase activity.

The present invention relates to isolated polypeptides havingendoglucanase activity selected from the group consisting of:

-   -   (a) a polypeptide having at least 60% sequence identity to the        polypeptide of SEQ ID NO: 26; at least 65% sequence identity to        the polypeptide of SEQ ID NO: 28; at least 70% sequence identity        to the polypeptide of SEQ ID NO: 30 or SEQ ID NO: 32; at least        80% sequence identity to the polypeptide of SEQ ID NO: 34, SEQ        ID NO: 36, or SEQ ID NO: 38; at least 85% sequence identity to        the polypeptide of SEQ ID NO: 40 or SEQ ID NO: 42; at least 97%        sequence identity to the polypeptide of SEQ ID NO: 44; or at        least 98% sequence identity to the polypeptide of SEQ ID NO: 46;    -   (b) a polypeptide encoded by a polynucleotide that hybridizes        under at least high stringency conditions with (i) the        polypeptide coding sequence of SEQ ID NO: 25 or SEQ ID NO:        27, (ii) the cDNA sequence thereof, or (iii) the full-length        complement of (i) or (ii); or under at least very high        stringency conditions with (i) the polypeptide coding sequence        of SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35,        SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, or        SEQ ID NO: 45, (ii) the cDNA sequence thereof, or (iii) the        full-length complement of (i) or (ii);    -   (c) a polypeptide encoded by a polynucleotide having at least        60% sequence identity to the polypeptide coding sequence of SEQ        ID NO: 25 or the cDNA sequence thereof; at least 65% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 27 or        the cDNA sequence thereof; at least 70% sequence identity to the        polypeptide coding sequence of SEQ ID NO: 29 or SEQ ID NO: 31,        or the cDNA sequences thereof; at least 80% sequence identity to        the polypeptide coding sequence of SEQ ID NO: 33, SEQ ID NO: 35,        or SEQ ID NO: 37, or the cDNA sequences thereof; at least 85%        sequence identity to the polypeptide coding sequence of SEQ ID        NO: 39 or SEQ ID NO: 41, or the cDNA sequences thereof; at least        97% sequence identity to the polypeptide coding sequence of SEQ        ID NO: 43 or the cDNA sequence thereof; or at least 98% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 45 or        the cDNA sequence thereof;    -   (d) a variant comprising the polypeptide of SEQ ID NO: 26, SEQ        ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID        NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO:        44, or SEQ ID NO: 46 comprising a substitution, deletion, and/or        insertion at one or more (e.g., several) positions; and    -   (e) a fragment of the polypeptide of (a), (b), (c), or (d) that        has endoglucanase activity.

The present invention relates to isolated GH61 polypeptides havingcellulolytic enhancing activity selected from the group consisting of:

-   -   (a) a polypeptide having at least 70% sequence identity to the        polypeptide of SEQ ID NO: 48; at least 75% sequence identity to        the polypeptide of SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54,        or SEQ ID NO: 79; at least 80% sequence identity to the        polypeptide of SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ        ID NO: 62, or SEQ ID NO: 64; at least 85% sequence identity to        the polypeptide of SEQ ID NO: 66; or at least 90% sequence        identity to the polypeptide of SEQ ID NO: 68, SEQ ID NO: 70, or        SEQ ID NO: 72;    -   (b) a polypeptide encoded by a polynucleotide that hybridizes        under at least very high stringency conditions with (i) the        polypeptide coding sequence of SEQ ID NO: 47, SEQ ID NO: 49, SEQ        ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID        NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO:        67, SEQ ID NO: 69, or SEQ ID NO: 71, (ii) the cDNA sequence        thereof, or (iii) the full-length complement of (i) or (ii);    -   (c) a polypeptide encoded by a polynucleotide having at least        70% sequence identity to the polypeptide coding sequence of SEQ        ID NO: 47 or the cDNA sequence thereof; at least 75% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 49,        SEQ ID NO: 51, or SEQ ID NO: 53, or the cDNA sequences thereof;        at least 80% sequence identity to the polypeptide coding        sequence of SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID        NO: 61, or SEQ ID NO: 63, or the cDNA sequences thereof; at        least 85% sequence identity to the polypeptide coding sequence        of SEQ ID NO: 65 or the cDNA sequence thereof; or at least 90%        sequence identity to the polypeptide coding sequence of SEQ ID        NO: 67, SEQ ID NO: 69, or SEQ ID NO: 71, or the cDNA sequences        thereof;    -   (d) a variant comprising the polypeptide of SEQ ID NO: 48, SEQ        ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID        NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO:        66, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO:        79 comprising a substitution, deletion, and/or insertion at one        or more (e.g., several) positions; and    -   (e) a fragment of the polypeptide of (a), (b), (c), or (d) that        has cellulolytic enhancing activity.

The present invention relates to isolated polypeptides having xylanaseactivity selected from the group consisting of:

-   -   (a) a polypeptide having at least 70% sequence identity to the        polypeptide of SEQ ID NO: 74, at least 94% sequence identity to        the polypeptide of SEQ ID NO: 78, or at least 98% sequence        identity to the polypeptide of SEQ ID NO: 76;    -   (b) a polypeptide encoded by a polynucleotide that hybridizes        under at least very high stringency conditions with (i) the        polypeptide coding sequence of SEQ ID NO: 73, SEQ ID NO: 75, or        SEQ ID NO: 77, (ii) the cDNA sequence thereof, or (iii) the        full-length complement of (i) or (ii);    -   (c) a polypeptide encoded by a polynucleotide having at least        70% sequence identity to the polypeptide coding sequence of SEQ        ID NO: 73 or the cDNA sequence thereof, at least 94% sequence        identity to the polypeptide coding sequence of SEQ ID NO: 77 or        the cDNA sequence thereof, or at least 98% sequence identity to        the polypeptide coding sequence of SEQ ID NO: 75 or the cDNA        sequence thereof;    -   (d) a variant comprising the polypeptide of SEQ ID NO: 74, SEQ        ID NO: 76, or SEQ ID NO: 78 comprising a substitution, deletion,        and/or insertion at one or more (e.g., several) positions; and    -   (e) a fragment of the polypeptide of (a), (b), (c), or (d) that        has xylanase activity.

The present invention also relates to isolated polynucleotides encodingthe polypeptides of the present invention; nucleic acid constructs,recombinant expression vectors, and recombinant host cells comprisingthe polynucleotides; and methods of producing the polypeptides.

The present invention also relates to processes for degrading orconverting a cellulosic or xylan-containing material, comprising:treating the cellulosic or xylan-containing material with an enzymecomposition in the presence of a polypeptide having cellobiohydrolase,endoglucanase, cellulolytic enhancing, or xylanase activity of thepresent invention. In one aspect, the processes further compriserecovering the degraded or converted cellulosic or xylan-containingmaterial.

The present invention also relates to processes of producing afermentation product, comprising: (a) saccharifying a cellulosic orxylan-containing material with an enzyme composition in the presence ofa polypeptide having cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity of the present invention; (b) fermentingthe saccharified cellulosic or xylan-containing material with one ormore (e.g., several) fermenting microorganisms to produce thefermentation product; and (c) recovering the fermentation product fromthe fermentation.

The present invention also relates to processes of fermenting acellulosic or xylan-containing material, comprising: fermenting thecellulosic or xylan-containing material with one or more (e.g., several)fermenting microorganisms, wherein the cellulosic or xylan-containingmaterial is saccharified with an enzyme composition in the presence of apolypeptide having cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity of the present invention. In one aspect,the fermenting of the cellulosic or xylan-containing material produces afermentation product. In another aspect, the processes further compriserecovering the fermentation product from the fermentation.

Definitions

Acetylxylan esterase: The term “acetylxylan esterase” means acarboxylesterase (EC 3.1.1.72) that catalyzes the hydrolysis of acetylgroups from polymeric xylan, acetylated xylose, acetylated glucose,alpha-napthyl acetate, and p-nitrophenyl acetate. For purposes of thepresent invention, acetylxylan esterase activity is determined using 0.5mM p-nitrophenylacetate as substrate in 50 mM sodium acetate pH 5.0containing 0.01% TWEEN™ 20 (polyoxyethylene sorbitan monolaurate). Oneunit of acetylxylan esterase is defined as the amount of enzyme capableof releasing 1 μmole of p-nitrophenolate anion per minute at pH 5, 25°C.

Allelic variant: The term “allelic variant” means any of two or morealternative forms of a gene occupying the same chromosomal locus.Allelic variation arises naturally through mutation, and may result inpolymorphism within populations. Gene mutations can be silent (no changein the encoded polypeptide) or may encode polypeptides having alteredamino acid sequences. An allelic variant of a polypeptide is apolypeptide encoded by an allelic variant of a gene.

Alpha-L-arabinofuranosidase: The term “alpha-L-arabinofuranosidase”means an alpha-L-arabinofuranoside arabinofuranohydrolase (EC 3.2.1.55)that catalyzes the hydrolysis of terminal non-reducingalpha-L-arabinofuranoside residues in alpha-L-arabinosides. The enzymeacts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)-and/or (1,5)-linkages, arabinoxylans, and arabinogalactans.Alpha-L-arabinofuranosidase is also known as arabinosidase,alpha-arabinosidase, alpha-L-arabinosidase, alpha-arabinofuranosidase,polysaccharide alpha-L-arabinofuranosidase, alpha-L-arabinofuranosidehydrolase, L-arabinosidase, or alpha-L-arabinanase. For purposes of thepresent invention, alpha-L-arabinofuranosidase activity is determinedusing 5 mg of medium viscosity wheat arabinoxylan (MegazymeInternational Ireland, Ltd., Bray, Co. Wicklow, Ireland) per ml of 100mM sodium acetate pH 5 in a total volume of 200 μl for 30 minutes at 40°C. followed by arabinose analysis by AMINEX® HPX-87H columnchromatography (Bio-Rad Laboratories, Inc., Hercules, Calif., USA).

Alpha-glucuronidase: The term “alpha-glucuronidase” means analpha-D-glucosiduronate glucuronohydrolase (EC 3.2.1.139) that catalyzesthe hydrolysis of an alpha-D-glucuronoside to D-glucuronate and analcohol. For purposes of the present invention, alpha-glucuronidaseactivity is determined according to de Vries, 1998, J. Bacteriol. 180:243-249. One unit of alpha-glucuronidase equals the amount of enzymecapable of releasing 1 μmole of glucuronic or 4-O-methylglucuronic acidper minute at pH 5, 40° C.

Amino acid sequence: The term “amino acid sequence” means the order inwhich amino acid residues, connected by peptide bonds, lie in the chainsof peptides and proteins. The sequence is generally reported from theN-terminal end containing a free amino group to the C-terminal endcontaining a free carboxyl group. Single letter amino acid codes areused. The code “X” is used to designate one or more residues of anyamino acid. Single letter nucleic acid codes are used. The code “n” isused to designate one or more residues of any nucleic acid.

Beta-glucosidase: The term “beta-glucosidase” means a beta-D-glucosideglucohydrolase (E.C. 3.2.1.21) that catalyzes the hydrolysis of terminalnon-reducing beta-D-glucose residues with the release of beta-D-glucose.For purposes of the present invention, beta-glucosidase activity isdetermined using p-nitrophenyl-beta-D-glucopyranoside as substrateaccording to the procedure of Venturi et al., 2002, Extracellularbeta-D-glucosidase from Chaetomium thermophilum var. coprophilum:production, purification and some biochemical properties, J. BasicMicrobiol. 42: 55-66. One unit of beta-glucosidase is defined as 1.0μmole of p-nitrophenolate anion produced per minute at 25° C., pH 4.8from 1 mM p-nitrophenyl-beta-D-glucopyranoside as substrate in 50 mMsodium citrate containing 0.01% TWEEN® 20.

Beta-xylosidase: The term “beta-xylosidase” means a beta-D-xylosidexylohydrolase (E.C. 3.2.1.37) that catalyzes the exo-hydrolysis of shortbeta (1→4)-xylooligosaccharides to remove successive D-xylose residuesfrom non-reducing termini. For purposes of the present invention, oneunit of beta-xylosidase is defined as 1.0 μmole of p-nitrophenolateanion produced per minute at 40° C., pH 5 from 1 mMp-nitrophenyl-beta-D-xyloside as substrate in 100 mM sodium citratecontaining 0.01% TWEEN® 20.

cDNA: The term “cDNA” means a DNA molecule that can be prepared byreverse transcription from a mature, spliced, mRNA molecule obtainedfrom a eukaryotic or prokaryotic cell. cDNA lacks intron sequences thatmay be present in the corresponding genomic DNA. The initial, primaryRNA transcript is a precursor to mRNA that is processed through a seriesof steps, including splicing, before appearing as mature spliced mRNA.

Cellobiohydrolase: The term “cellobiohydrolase” means a1,4-beta-D-glucan cellobiohydrolase (E.C. 3.2.1.91 and E.C. 3.2.1.176)that catalyzes the hydrolysis of 1,4-beta-D-glucosidic linkages incellulose, cellooligosaccharides, or any beta-1,4-linked glucosecontaining polymer, releasing cellobiose from the reducing ornon-reducing ends of the chain (Teeri, 1997, Crystalline cellulosedegradation: New insight into the function of cellobiohydrolases, Trendsin Biotechnology 15: 160-167; Teeri et al., 1998, Trichoderma reeseicellobiohydrolases: why so efficient on crystalline cellulose?, Biochem.Soc. Trans. 26: 173-178). Cellobiohydrolase activity is determinedaccording to the procedures described by Lever et al., 1972, Anal.Biochem. 47: 273-279; van Tilbeurgh et al., 1982, FEBS Letters, 149:152-156; van Tilbeurgh and Claeyssens, 1985, FEBS Letters, 187: 283-288;and Tomme et al., 1988, Eur. J. Biochem. 170: 575-581.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the cellobiohydrolaseactivity of the polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6,SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, or SEQ ID NO: 24.

Cellulosic material: The term “cellulosic material” means any materialcontaining cellulose. The predominant polysaccharide in the primary cellwall of biomass is cellulose, the second most abundant is hemicellulose,and the third is pectin. The secondary cell wall, produced after thecell has stopped growing, also contains polysaccharides and isstrengthened by polymeric lignin covalently cross-linked tohemicellulose. Cellulose is a homopolymer of anhydrocellobiose and thusa linear beta-(1-4)-D-glucan, while hemicelluloses include a variety ofcompounds, such as xylans, xyloglucans, arabinoxylans, and mannans incomplex branched structures with a spectrum of substituents. Althoughgenerally polymorphous, cellulose is found in plant tissue primarily asan insoluble crystalline matrix of parallel glucan chains.Hemicelluloses usually hydrogen bond to cellulose, as well as to otherhemicelluloses, which help stabilize the cell wall matrix.

Cellulose is generally found, for example, in the stems, leaves, hulls,husks, and cobs of plants or leaves, branches, and wood of trees. Thecellulosic material can be, but is not limited to, agricultural residue,herbaceous material (including energy crops), municipal solid waste,pulp and paper mill residue, waste paper, and wood (including forestryresidue) (see, for example, Wiselogel et al., 1995, in Handbook onBioethanol (Charles E. Wyman, editor), pp. 105-118, Taylor & Francis,Washington D.C.; Wyman, 1994, Bioresource Technology 50: 3-16; Lynd,1990, Applied Biochemistry and Biotechnology 24/25: 695-719; Mosier etal., 1999, Recent Progress in Bioconversion of Lignocellulosics, inAdvances in Biochemical Engineering/Biotechnology, T. Scheper, managingeditor, Volume 65, pp. 23-40, Springer-Verlag, New York). It isunderstood herein that the cellulose may be in the form oflignocellulose, a plant cell wall material containing lignin, cellulose,and hemicellulose in a mixed matrix. In a preferred aspect, thecellulosic material is any biomass material. In another preferredaspect, the cellulosic material is lignocellulose, which comprisescellulose, hemicelluloses, and lignin.

In one aspect, the cellulosic material is agricultural residue. Inanother aspect, the cellulosic material is herbaceous material(including energy crops). In another aspect, the cellulosic material ismunicipal solid waste. In another aspect, the cellulosic material ispulp and paper mill residue. In another aspect, the cellulosic materialis waste paper. In another aspect, the cellulosic material is wood(including forestry residue).

In another aspect, the cellulosic material is arundo. In another aspect,the cellulosic material is bagasse. In another aspect, the cellulosicmaterial is bamboo. In another aspect, the cellulosic material is corncob. In another aspect, the cellulosic material is corn fiber. Inanother aspect, the cellulosic material is corn stover. In anotheraspect, the cellulosic material is miscanthus. In another aspect, thecellulosic material is orange peel. In another aspect, the cellulosicmaterial is rice straw. In another aspect, the cellulosic material isswitchgrass. In another aspect, the cellulosic material is wheat straw.

In another aspect, the cellulosic material is aspen. In another aspect,the cellulosic material is eucalyptus. In another aspect, the cellulosicmaterial is fir. In another aspect, the cellulosic material is pine. Inanother aspect, the cellulosic material is poplar. In another aspect,the cellulosic material is spruce. In another aspect, the cellulosicmaterial is willow.

In another aspect, the cellulosic material is algal cellulose. Inanother aspect, the cellulosic material is bacterial cellulose. Inanother aspect, the cellulosic material is cotton linter. In anotheraspect, the cellulosic material is filter paper. In another aspect, thecellulosic material is microcrystalline cellulose. In another aspect,the cellulosic material is phosphoric-acid treated cellulose.

In another aspect, the cellulosic material is an aquatic biomass. Asused herein the term “aquatic biomass” means biomass produced in anaquatic environment by a photosynthesis process. The aquatic biomass canbe algae, emergent plants, floating-leaf plants, or submerged plants.

The cellulosic material may be used as is or may be subjected topretreatment, using conventional methods known in the art, as describedherein. In a preferred aspect, the cellulosic material is pretreated.

In another aspect, degrading or converting of a cellulosic material isperformed in a bioreactor or in situ, i.e., in the place where thecellulosic material naturally occurs.

Cellulolytic enzyme or cellulase or cellulose-degrading polypeptide: Theterm “cellulolytic enzyme” or “cellulase” or “cellulose-degradingpolypeptide” means one or more (e.g., several) enzymes that hydrolyze acellulosic material. Such enzymes may include endoglucanase(s),cellobiohydrolase(s), beta-glucosidase(s), or combinations thereof. Theterm refers broadly to enzymes exhibiting cellulase or cellulolyticactivity such as glycoside hydrolases (GHs) and to enzymes with capacityto enhance the breakdown of lignocellulose when used in conjunction witha cellulase or a mixture of cellulases. Cellulose-degrading proteinsexhibit catalytic or other activity making the protein able to by itselfor together with other proteins or with catalysts to convert celluloseto smaller cellulose chains or to monomeric sugars. Examples of suchenzymes, but not limited to, are represented by glycoside hydrolases(GHs) of the Carbohydrate-Active Enzymes database (CAZy). Thus,polypeptides of the GH6, GH7, GH10, GH45, and GH61 families are hereinreferred to as cellulose-degrading polypeptides.

The two basic approaches for measuring cellulolytic activity include:(1) measuring the total cellulolytic activity, and (2) measuring theindividual cellulolytic activities (endoglucanases, cellobiohydrolases,and beta-glucosidases) as reviewed in Zhang et al., Outlook forcellulase improvement: Screening and selection strategies, 2006,Biotechnology Advances 24: 452-481. Total cellulolytic activity isusually measured using insoluble substrates, including Whatman No 1filter paper, microcrystalline cellulose, bacterial cellulose, algalcellulose, cotton, pretreated lignocellulose, etc. The most common totalcellulolytic activity assay is the filter paper assay using Whatman No 1filter paper as the substrate. The assay was established by theInternational Union of Pure and Applied Chemistry (IUPAC) (Ghose, 1987,Measurement of cellulase activities, Pure Appl. Chem. 59: 257-68).

For purposes of the present invention, cellulolytic enzyme activity isdetermined by measuring the increase in hydrolysis of a cellulosicmaterial by cellulolytic enzyme(s) under the following conditions: 1-50mg of cellulolytic enzyme protein/g of cellulose in PCS (or otherpretreated cellulosic material) for 3-7 days at a suitable temperature,e.g., 50° C., 55° C., or 60° C., compared to a control hydrolysiswithout addition of cellulolytic enzyme protein. Typical conditions are1 ml reactions, washed or unwashed PCS, 5% insoluble solids, 50 mMsodium acetate pH 5, 1 mM MnSO₄, 50° C., 55° C., or 60° C., 72 hours,sugar analysis by AMINEX® HPX-87H column (Bio-Rad Laboratories, Inc.,Hercules, Calif., USA).

Coding sequence: The term “coding sequence” means a polynucleotide,which directly specifies the amino acid sequence of a polypeptide. Theboundaries of the coding sequence are generally determined by an openreading frame, which begins with a start codon such as ATG, GTG, or TTGand ends with a stop codon such as TAA, TAG, or TGA. The coding sequencemay be a genomic DNA, cDNA, synthetic DNA, or a combination thereof.

Complementarity: In molecular biology the term “complementarity” is aproperty of double-stranded nucleic acids such as DNA and RNA as well asDNA:RNA duplexes. Each strand is complementary to the other in that thebase pairs between them are non-covalently connected via two or threehydrogen bonds. For DNA, adenosine (A) bases complement thymine (T)bases and vice versa; guanine (G) bases complement cytosine (C) basesand vice versa. With RNA, it is the same except that adenine (A) basescomplement uracil (U) bases instead of thymine (T) bases.

Since there is only one complementary base for each of the bases foundin DNA and in RNA, one can reconstruct a complementary strand for anysingle strand. All C bases in one strand will pair with G bases in thecomplementary strand, etc. This is essential for DNA replication.

For example, the complementary strand of the DNA sequence 5′ A G T C A TG 3′ is 3′ T C A G T A C 5′.

The sequence 5′ C A T G A C T 3′ is called the reverse complementarystrand to the DNA sequence 5′ A G T C A T G 3′ when it is written withthe 5′ end on the left and the 3′ end on the right

Sequences of degenerate nucleotides such as in primers are representedaccording to the IUPAC code for degenerate nucleotides: A: Adenine, C:Cytosine, D: A, G, or T (A/G/T), G: Guanine, H: A, C, or T (A/C/T), K: Gor T (G/T), M: A or C (A/C), N: A, C, G, or T (A/C/G/T), R: A or G(A/G), S: C or G (C/G), T: Thymine, V: A, C, or G(A/C/G), W: A or T(A/T), Y: C or T (C/T).

Composition: The term “composition” means a mixture of two or more(e.g., several) substances, e.g., enzymes.

Control sequences: The term “control sequences” means nucleic acidsequences necessary for expression of a polynucleotide encoding apolypeptide of the present invention. Each control sequence may benative (i.e., from the same gene) or foreign (i.e., from a differentgene) to the polynucleotide encoding the polypeptide or native orforeign to each other. Such control sequences include, but are notlimited to, a leader, polyadenylation sequence, propeptide sequence,promoter, signal peptide sequence, and transcription terminator. At aminimum, the control sequences include a promoter, and transcriptionaland translational stop signals. The control sequences may be providedwith linkers for the purpose of introducing specific restriction sitesfacilitating ligation of the control sequences with the coding region ofthe polynucleotide encoding a polypeptide.

Endoglucanase: The term “endoglucanase” means anendo-1,4-(1,3;1,4)-beta-D-glucan 4-glucanohydrolase (E.C. 3.2.1.4) thatcatalyzes endohydrolysis of 1,4-beta-D-glycosidic linkages in cellulose,cellulose derivatives (such as carboxymethyl cellulose and hydroxyethylcellulose), lichenin, beta-1,4 bonds in mixed beta-1,3 glucans such ascereal beta-D-glucans or xyloglucans, and other plant materialcontaining cellulosic components. Endoglucanase activity can bedetermined by measuring reduction in substrate viscosity or increase inreducing ends determined by a reducing sugar assay (Zhang et al., 2006,Biotechnology Advances 24: 452-481). For purposes of the presentinvention, endoglucanase activity is determined using carboxymethylcellulose (CMC) as substrate according to the procedure of Ghose, 1987,Pure and Appl. Chem. 59: 257-268, at pH 5, 40° C.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the endoglucanase activityof the polypeptide of SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40,SEQ ID NO: 42, SEQ ID NO: 44, or SEQ ID NO: 46.

Expression: The term “expression” includes any step involved in theproduction of a polypeptide including, but not limited to,transcription, post-transcriptional modification, translation,post-translational modification, and secretion.

Expression vector: The term “expression vector” means a linear orcircular DNA molecule that comprises a polynucleotide encoding apolypeptide and is operably linked to control sequences that provide forits expression.

Family 6 glycoside hydrolase: The term “Family 6 glycoside hydrolase” or“Family GH6” or “GH6” means a polypeptide falling into the glycosidehydrolase Family 6 according to Henrissat B., 1991, A classification ofglycosyl hydrolases based on amino-acid sequence similarities, Biochem.J. 280: 309-316, and Henrissat B., and Bairoch A., 1996, Updating thesequence-based classification of glycosyl hydrolases, Biochem. J. 316:695-696.

Family 7 glycoside hydrolase: The term “Family 7 glycoside hydrolase” or“Family GH7” or “GH7” means a polypeptide falling into the glycosidehydrolase Family 7 according to Henrissat, 1991, supra, and Henrissatand Bairoch, 1996, supra.

Family 10 glycoside hydrolase: The term “Family 10 glycoside hydrolase”or “Family GH10” or “GH10” means a polypeptide falling into theglycoside hydrolase Family 10 according to Henrissat, 1991, supra, andHenrissat and Bairoch, 1996, supra.

Family 45 glycoside hydrolase: The term “Family 45 glycoside hydrolase”or “Family GH45” or “GH45” means a polypeptide falling into theglycoside hydrolase Family 45 according to Henrissat, 1991, supra, andHenrissat and Bairoch, 1996, supra.

Family 61 glycoside hydrolase: The term “Family 61 glycoside hydrolase”or “Family GH61” or “GH61” means a polypeptide falling into theglycoside hydrolase Family 61 according to Henrissat, 1991, supra, andHenrissat and Bairoch, 1996, supra. The enzymes in this family wereoriginally classified as a glycoside hydrolase family based onmeasurement of very weak endo-1,4-beta-D-glucanase activity in onefamily member. The structure and mode of action of these enzymes arenon-canonical and they cannot be considered as bona fide glycosidases.However, they are kept in the CAZy classification on the basis of theircapacity to enhance the breakdown of lignocellulose when used inconjunction with a cellulase or a mixture of cellulases.

Feruloyl esterase: The term “feruloyl esterase” means a4-hydroxy-3-methoxycinnamoyl-sugar hydrolase (EC 3.1.1.73) thatcatalyzes the hydrolysis of 4-hydroxy-3-methoxycinnamoyl (feruloyl)groups from esterified sugar, which is usually arabinose in naturalbiomass substrates, to produce ferulate (4-hydroxy-3-methoxycinnamate).Feruloyl esterase is also known as ferulic acid esterase,hydroxycinnamoyl esterase, FAE-III, cinnamoyl ester hydrolase, FAEA,cinnAE, FAE-I, or FAE-II. For purposes of the present invention,feruloyl esterase activity is determined using 0.5 mMp-nitrophenylferulate as substrate in 50 mM sodium acetate pH 5.0. Oneunit of feruloyl esterase equals the amount of enzyme capable ofreleasing 1 μmole of p-nitrophenolate anion per minute at pH 5, 25° C.

Fragment: The term “fragment” means a polypeptide having one or more(e.g., several) amino acids absent from the amino and/or carboxylterminus of a polypeptide; wherein the fragment has cellobiohydrolase,endoglucanase, cellulolytic enhancing, or xylanase activity. In oneaspect, a fragment contains at least 85% of the amino acid residues,e.g., at least 90% of the amino acid residues or at least 90% of theamino acid residues of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ IDNO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26,SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO:36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ IDNO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64,SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 74, SEQ ID NO:76, SEQ ID NO: 78, or SEQ ID NO: 79.

Hemicellulolytic enzyme or hemicellulase: The term “hemicellulolyticenzyme” or “hemicellulase” means one or more (e.g., several) enzymesthat hydrolyze a hemicellulosic material. See, for example, Shallom, D.and Shoham, Y. Microbial hemicellulases. Current Opinion InMicrobiology, 2003, 6(3): 219-228). Hemicellulases are key components inthe degradation of plant biomass. Examples of hemicellulases include,but are not limited to, an acetylmannan esterase, an acetylxylanesterase, an arabinanase, an arabinofuranosidase, a coumaric acidesterase, a feruloyl esterase, a galactosidase, a glucuronidase, aglucuronoyl esterase, a mannanase, a mannosidase, a xylanase, and axylosidase. The substrates of these enzymes, the hemicelluloses, are aheterogeneous group of branched and linear polysaccharides that arebound via hydrogen bonds to the cellulose microfibrils in the plant cellwall, crosslinking them into a robust network. Hemicelluloses are alsocovalently attached to lignin, forming together with cellulose a highlycomplex structure. The variable structure and organization ofhemicelluloses require the concerted action of many enzymes for itscomplete degradation. The catalytic modules of hemicellulases are eitherglycoside hydrolases (GHs) that hydrolyze glycosidic bonds, orcarbohydrate esterases (CEs), which hydrolyze ester linkages of acetateor ferulic acid side groups. These catalytic modules, based on homologyof their primary sequence, can be assigned into GH and CE families. Somefamilies, with an overall similar fold, can be further grouped intoclans, marked alphabetically (e.g., GH-A). A most informative andupdated classification of these and other carbohydrate active enzymes isavailable in the Carbohydrate-Active Enzymes (CAZy) database.Hemicellulolytic enzyme activities can be measured according to Ghoseand Bisaria, 1987, Pure & Appl. Chem. 59: 1739-1752, at a suitabletemperature, e.g., 50° C., 55° C., or 60° C., and pH, e.g., 5.0 or 5.5.

High stringency conditions: The term “high stringency conditions” meansfor probes of at least 100 nucleotides in length, prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml shearedand denatured salmon sperm DNA, and 50% formamide, following standardSouthern blotting procedures for 12 to 24 hours. The carrier material isfinally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at65° C.

Host cell: The term “host cell” means any cell type that is susceptibleto transformation, transfection, transduction, or the like with anucleic acid construct or expression vector comprising a polynucleotideof the present invention. The term “host cell” encompasses any progenyof a parent cell that is not identical to the parent cell due tomutations that occur during replication.

Isolated: The term “isolated” means a substance in a form or environmentthat does not occur in nature. Non-limiting examples of isolatedsubstances include (1) any non-naturally occurring substance, (2) anysubstance including, but not limited to, any enzyme, variant, nucleicacid, protein, peptide or cofactor, that is at least partially removedfrom one or more or all of the naturally occurring constituents withwhich it is associated in nature; (3) any substance modified by the handof man relative to that substance found in nature; or (4) any substancemodified by increasing the amount of the substance relative to othercomponents with which it is naturally associated (e.g., multiple copiesof a gene encoding the substance; use of a stronger promoter than thepromoter naturally associated with the gene encoding the substance). Thepolypeptide of the present invention may be used in industrialapplications in the form of a fermentation broth product, that is, thepolypeptide of the present invention is a component of a fermentationbroth used as a product in industrial applications (e.g., ethanolproduction). The fermentation broth product will in addition to thepolypeptide of the present invention comprise additional ingredientsused in the fermentation process, such as, for example, cells(including, the host cells containing the gene encoding the polypeptideof the present invention which are used to produce the polypeptide ofinterest), cell debris, biomass, fermentation media and/or fermentationproducts. The fermentation broth may optionally be subjected to one ormore purification (including filtration) steps to remove or reduce onemore components of a fermentation process. Accordingly, an isolatedsubstance may be present in such a fermentation broth product.

Low stringency conditions: The term “low stringency conditions” meansfor probes of at least 100 nucleotides in length, prehybridization andhybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml shearedand denatured salmon sperm DNA, and 25% formamide, following standardSouthern blotting procedures for 12 to 24 hours. The carrier material isfinally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at50° C.

Mature polypeptide: The term “mature polypeptide” means a polypeptide inits final form following translation and any post-translationalmodifications, such as N-terminal processing, C-terminal truncation,glycosylation, phosphorylation, etc. It is known in the art that a hostcell may produce a mixture of two of more different mature polypeptides(i.e., with a different C-terminal and/or N-terminal amino acid)expressed by the same polynucleotide.

Mature polypeptide coding sequence: The term “mature polypeptide codingsequence” means a polynucleotide that encodes a mature polypeptidehaving cellobiohydrolase, endoglucanase, cellulolytic enhancing, orxylanase activity.

Medium stringency conditions: The term “medium stringency conditions”means for probes of at least 100 nucleotides in length, prehybridizationand hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/mlsheared and denatured salmon sperm DNA, and 35% formamide, followingstandard Southern blotting procedures for 12 to 24 hours. The carriermaterial is finally washed three times each for 15 minutes using 2×SSC,0.2% SDS at 55° C.

Medium-high stringency conditions: The term “medium-high stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 35% formamide,following standard Southern blotting procedures for 12 to 24 hours. Thecarrier material is finally washed three times each for 15 minutes using2×SSC, 0.2% SDS at 60° C.

Nucleic acid construct: The term “nucleic acid construct” means anucleic acid molecule, either single- or double-stranded, which isisolated from a naturally occurring gene or is modified to containsegments of nucleic acids in a manner that would not otherwise exist innature or which is synthetic, which comprises one or more controlsequences.

Operably linked: The term “operably linked” means a configuration inwhich a control sequence is placed at an appropriate position relativeto the coding sequence of a polynucleotide such that the controlsequence directs expression of the coding sequence.

Peptide: The term “peptide” means a smaller peptide comprising fewerthan about 20 consecutive amino acids.

Polynucleotide: The term “polynucleotide” means to a nucleic acidsequence that comprises more than about 30 consecutive nucleotides ormodified nucleotides. Polynucleotides include DNA, RNA, m-RNA, r-RNA,t-RNA, cDNA, DNA-RNA duplexes, etc.

Polypeptide: The term “polypeptide” means a longer peptide thatcomprises more than about 20 consecutive amino acids. The term“polypeptide” encompasses proteins, fragments of proteins, cleaved formsof proteins, partially digested proteins, and the like, which aregreater than about 20 consecutive amino acids.

Polypeptide having cellulolytic enhancing activity: The term“polypeptide having cellulolytic enhancing activity” means a GH61polypeptide that catalyzes the enhancement of the hydrolysis of acellulosic material by enzyme having cellulolytic activity. For purposesof the present invention, cellulolytic enhancing activity is determinedby measuring the increase in reducing sugars or the increase of thetotal of cellobiose and glucose from the hydrolysis of a cellulosicmaterial by cellulolytic enzyme under the following conditions: 1-50 mgof total protein/g of cellulose in PCS, wherein total protein iscomprised of 50-99.5% w/w cellulolytic enzyme protein and 0.5-50% w/wprotein of a GH61 polypeptide having cellulolytic enhancing activity for1-7 days at a suitable temperature, e.g., 50° C., 55° C., or 60° C., andpH, e.g., 5.0 or 5.5, compared to a control hydrolysis with equal totalprotein loading without cellulolytic enhancing activity (1-50 mg ofcellulolytic protein/g of cellulose in PCS). In a preferred aspect, amixture of CELLUCLAST® 1.5 L (Novozymes A/S, Bagsværd, Denmark) in thepresence of 2-3% of total protein weight Aspergillus oryzaebeta-glucosidase (recombinantly produced in Aspergillus oryzae accordingto WO 02/095014) or 2-3% of total protein weight Aspergillus fumigatusbeta-glucosidase (recombinantly produced in Aspergillus oryzae asdescribed in WO 2002/095014) of cellulase protein loading is used as thesource of the cellulolytic activity.

The GH61 polypeptides having cellulolytic enhancing activity enhance thehydrolysis of a cellulosic material catalyzed by enzyme havingcellulolytic activity by reducing the amount of cellulolytic enzymerequired to reach the same degree of hydrolysis preferably at least1.01-fold, e.g., at least 1.05-fold, at least 1.10-fold, at least1.25-fold, at least 1.5-fold, at least 2-fold, at least 3-fold, at least4-fold, at least 5-fold, at least 10-fold, or at least 20-fold.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the cellulolytic enhancingactivity of the polypeptide of SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO:52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ IDNO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 70, SEQID NO: 72, or SEQ ID NO: 79.

Pretreated corn stover: The term “PCS” or “Pretreated Corn Stover” meansa cellulosic material derived from corn stover by treatment with heatand dilute sulfuric acid, alkaline pretreatment, or neutralpretreatment.

Sequence identity: The term “sequence identity” means a comparisonbetween pairs of nucleic acid or amino acid molecules, i.e., therelatedness between two amino acid sequences or between two nucleotidesequences. In general, the sequences are aligned so that the highestorder match is obtained. Methods for determining sequence identity areknown and can be determined by commercially available computer programsthat can calculate % identity between two or more sequences. A typicalexample of such a computer program is CLUSTAL. As an illustration, by apolynucleotide having a nucleotide sequence having at least, forexample, 90% sequence identity to a reference nucleotide sequence isintended that the nucleotide sequence of the polynucleotide is identicalto the reference sequence except that the polynucleotide sequence mayinclude on average of up to 10 point mutations per each 100 nucleotidesof the reference nucleotide sequence. In other words, to obtain apolynucleotide having a nucleotide sequence at least 90% identical to areference nucleotide sequence, up to 10% of the nucleotides in thereference sequence may be deleted or substituted with anothernucleotide, or a number of nucleotides up to 10% of the totalnucleotides in the reference sequence may be inserted into the referencesequence. These mutations of the reference sequence may occur at the 5′or 3′ terminal positions of the reference nucleotide sequence oranywhere between those terminal positions, interspersed eitherindividually among nucleotides in the reference sequence or in one ormore contiguous groups within the reference sequence. Similarly, by apolypeptide having an amino acid sequence having at least, for example,90% sequence identity to a reference amino acid sequence is intendedthat the amino acid sequence of the polypeptide is identical to thereference sequence except that the polypeptide sequence may include onaverage up to 10 amino acid alterations per each 100 amino acids of thereference amino acid. In other words, to obtain a polypeptide having anamino acid sequence at least 90% identical to a reference amino acidsequence, up to 10% of the amino acid residues in the reference sequencemay be deleted or substituted with another amino acid, or a number ofamino acids up to 10% of the total amino acid residues in the referencesequence may be inserted into the reference sequence. These alterationsof the reference sequence may occur at the amino or carboxy terminalpositions of the reference amino acid sequence or anywhere between thoseterminal positions, interspersed either individually among residues inthe reference sequence or in one or more contiguous groups within thereference sequence.

Preferred methods to determine identity are designed to give the largestmatch between the sequences tested. Methods to determine identity aredescribed in publicly available computer programs. Preferred computerprogram methods to determine identity between two sequences include theGCG program package, including GAP (Devereux et al., 1984, Nucl. Acid.Res. 12: 387; Genetics Computer Group, University of Wisconsin, Madison,Wis., USA), BLASTP, BLASTN, and FASTA (Altschul et al., 1990, J. Mol.Biol. 215: 403-410). The BLASTX program is publicly available from theNational Center for Biotechnology Information (NCBI) and other sources(BLAST Manual, Altschul et al. NCB/NLM/NIH Bethesda, Md., USA; Altschulet al., supra). The well-known Smith Waterman algorithm may also be usedto determine identity. For example, using the computer algorithm GAP(Genetics Computer Group, University of Wisconsin, Madison, Wis., USA),two proteins for which the percent sequence identity is to be determinedare aligned for optimal matching of their respective amino acids (the“matched span”, as determined by the algorithm). A gap opening penalty(which is calculated as 3 times the average diagonal; the “averagediagonal” is the average of the diagonal of the comparison matrix beingused; the “diagonal” is the score or number assigned to each perfectamino acid match by the particular comparison matrix) and a gapextension penalty (which is usually 1/10 times the gap opening penalty),as well as a comparison matrix such as PAM 250 or BLOSUM 62 are used inconjunction with the algorithm. A standard comparison matrix is alsoused by the algorithm (see Dayhoff et al., 1978, Atlas of ProteinSequence and Structure, Vol. 5, Suppl. 3, (1978) for the PAM 250comparison matrix; Henikoff et al., 1992, Proc. Natl. Acad. Sci USA 89:10915-10919, for the BLOSUM 62 comparison matrix).

For purposes of the present invention, the sequence identity between twoamino acid sequences is determined using the Needleman-Wunsch algorithm(Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implementedin the Needle program of the EMBOSS package (EMBOSS: The EuropeanMolecular Biology Open Software Suite, Rice et al., 2000, Trends Genet.16: 276-277), preferably version 5.0.0 or later. The parameters used aregap open penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62(EMBOSS version of BLOSUM62) substitution matrix. The output of Needlelabeled “longest identity” (obtained using the -nobrief option) is usedas the percent identity and is calculated as follows:(Identical Residues×100)/(Length of Alignment−Total Number of Gaps inAlignment)

For purposes of the present invention, the sequence identity between twodeoxyribonucleotide sequences is determined using the Needleman-Wunschalgorithm (Needleman and Wunsch, 1970, supra) as implemented in theNeedle program of the EMBOSS package (EMBOSS: The European MolecularBiology Open Software Suite, Rice et al., 2000, supra), preferablyversion 5.0.0 or later. The parameters used are gap open penalty of 10,gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBINUC4.4) substitution matrix. The output of Needle labeled “longestidentity” (obtained using the -nobrief option) is used as the percentidentity and is calculated as follows:(Identical Deoxyribonucleotides×100)/(Length of Alignment−Total Numberof Gaps in Alignment)

Subsequence: The term “subsequence” means a polynucleotide having one ormore (e.g., several) nucleotides absent from the 5′ and/or 3′ end of apolypeptide coding sequence; wherein the subsequence encodes a fragmenthaving cellobiohydrolase, endoglucanase, cellulolytic enhancing, orxylanase activity. In one aspect, a subsequence contains at least 85% ofthe nucleotides, e.g., at least 90% of the nucleotides or at least 95%of the nucleotides of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ IDNO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ IDNO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35,SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO:45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ IDNO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73,SEQ ID NO: 75, or SEQ ID NO: 77.

Variant: The term “variant” means a polypeptide havingcellobiohydrolase, endoglucanase, cellulolytic enhancing, or xylanaseactivity comprising an alteration, i.e., a substitution, insertion,and/or deletion, at one or more (e.g., several) positions. Asubstitution means replacement of the amino acid occupying a positionwith a different amino acid; a deletion means removal of the amino acidoccupying a position; and an insertion means adding an amino acidadjacent to and immediately following the amino acid occupying aposition.

Very high stringency conditions: The term “very high stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide,following standard Southern blotting procedures for 12 to 24 hours. Thecarrier material is finally washed three times each for 15 minutes using2×SSC, 0.2% SDS at 70° C.

Very low stringency conditions: The term “very low stringencyconditions” means for probes of at least 100 nucleotides in length,prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide,following standard Southern blotting procedures for 12 to 24 hours. Thecarrier material is finally washed three times each for 15 minutes using2×SSC, 0.2% SDS at 45° C.

Xylan-containing material: The term “xylan-containing material” meansany material comprising a plant cell wall polysaccharide containing abackbone of beta-(1-4)-linked xylose residues. Xylans of terrestrialplants are heteropolymers possessing a beta-(1-4)-D-xylopyranosebackbone, which is branched by short carbohydrate chains. They compriseD-glucuronic acid or its 4-O-methyl ether, L-arabinose, and/or variousoligosaccharides, composed of D-xylose, L-arabinose, D- or L-galactose,and D-glucose. Xylan-type polysaccharides can be divided into homoxylansand heteroxylans, which include glucuronoxylans,(arabino)glucuronoxylans, (glucurono)arabinoxylans, arabinoxylans, andcomplex heteroxylans. See, for example, Ebringerova et al., 2005, Adv.Polym. Sci. 186: 1-67.

In the processes of the present invention, any material containing xylanmay be used. In a preferred aspect, the xylan-containing material islignocellulose.

Xylan degrading activity or xylanolytic activity: The term “xylandegrading activity” or “xylanolytic activity” means a biologicalactivity that hydrolyzes xylan-containing material. The two basicapproaches for measuring xylanolytic activity include: (1) measuring thetotal xylanolytic activity, and (2) measuring the individual xylanolyticactivities (e.g., endoxylanases, beta-xylosidases, arabinofuranosidases,alpha-glucuronidases, acetylxylan esterases, feruloyl esterases, andalpha-glucuronyl esterases). Recent progress in assays of xylanolyticenzymes was summarized in several publications including Biely andPuchard, Recent progress in the assays of xylanolytic enzymes, 2006,Journal of the Science of Food and Agriculture 86(11): 1636-1647;Spanikova and Biely, 2006, Glucuronoyl esterase—Novel carbohydrateesterase produced by Schizophyllum commune, FEBS Letters 580(19):4597-4601; Herrmann, Vrsanska, Jurickova, Hirsch, Biely, and Kubicek,1997, The beta-D-xylosidase of Trichoderma reesei is a multifunctionalbeta-D-xylan xylohydrolase, Biochemical Journal 321: 375-381.

Total xylan degrading activity can be measured by determining thereducing sugars formed from various types of xylan, including, forexample, oat spelt, beechwood, and larchwood xylans, or by photometricdetermination of dyed xylan fragments released from various covalentlydyed xylans. The most common total xylanolytic activity assay is basedon production of reducing sugars from polymeric 4-O-methylglucuronoxylan as described in Bailey, Biely, Poutanen, 1992,Interlaboratory testing of methods for assay of xylanase activity,Journal of Biotechnology 23(3): 257-270. Xylanase activity can also bedetermined with 0.2% AZCL-arabinoxylan as substrate in 0.01% TRITON®X-100 (4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol) and 200mM sodium phosphate buffer pH 6 at 37° C. One unit of xylanase activityis defined as 1.0 μmole of azurine produced per minute at 37° C., pH 6from 0.2% AZCL-arabinoxylan as substrate in 200 mM sodium phosphate pH 6buffer.

For purposes of the present invention, xylan degrading activity isdetermined by measuring the increase in hydrolysis of birchwood xylan(Sigma Chemical Co., Inc., St. Louis, Mo., USA) by xylan-degradingenzyme(s) under the following typical conditions: 1 ml reactions, 5mg/ml substrate (total solids), 5 mg of xylanolytic protein/g ofsubstrate, 50 mM sodium acetate pH 5, 50° C., 24 hours, sugar analysisusing p-hydroxybenzoic acid hydrazide (PHBAH) assay as described byLever, 1972, A new reaction for colorimetric determination ofcarbohydrates, Anal. Biochem 47: 273-279.

Xylanase: The term “xylanase” means a 1,4-beta-D-xylan-xylohydrolase(E.C. 3.2.1.8) that catalyzes the endohydrolysis of 1,4-beta-D-xylosidiclinkages in xylans. For purposes of the present invention, xylanaseactivity is determined with 0.2% AZCL-arabinoxylan as substrate in 0.01%TRITON® X-100 and 200 mM sodium phosphate buffer pH 6 at 37° C. One unitof xylanase activity is defined as 1.0 μmole of azurine produced perminute at 37° C., pH 6 from 0.2% AZCL-arabinoxylan as substrate in 200mM sodium phosphate pH 6 buffer.

The polypeptides of the present invention have at least 20%, e.g., atleast 40%, at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95%, and at least 100% of the xylanase activity ofthe polypeptide of SEQ ID NO: 74, SEQ ID NO: 76, or SEQ ID NO: 78.

DETAILED DESCRIPTION OF THE INVENTION

Polypeptides Having Cellobiohydrolase, Endoglucanase, CellulolyticEnhancing, or Xylanase Activity

In an embodiment, the present invention relates to isolated polypeptideshaving at least 80%, e.g., at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 2or SEQ ID NO: 4; at least 90%, e.g., at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 6; at least 91%, e.g., at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 8; or atleast 99%, e.g., 100% sequence identity to the polypeptide of SEQ ID NO:10, which have cellobiohydrolase activity. In one aspect, thepolypeptides differ by up to 10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, or 10, from the polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ IDNO: 6, SEQ ID NO: 8, or SEQ ID NO: 10.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 2; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 2.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 4; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 4.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 6; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 6.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 8; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 8.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 10; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 10.

In another embodiment, the present invention relates to isolatedpolypeptides having at least 70%, e.g., at least 75%, at least 80%, atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 12; at least 80%, e.g., atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 14 or SEQ ID NO: 16; at least91%, e.g., at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 18; at least 96%, e.g., atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 20; or at least 98%, e.g., at least 99% or100% sequence identity to the polypeptide of SEQ ID NO: 22 or SEQ ID NO:24, which have cellobiohydrolase activity. In one aspect, thepolypeptides differ by up to 10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, or 10, from the polypeptide of SEQ ID NO: 12, SEQ ID NO: 14, SEQID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, or SEQ ID NO:24.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 12; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 12.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 14; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 14.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 16; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 16.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 18; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 18.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 20; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 20.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 22; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 22.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 24; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 24.

In another embodiment, the present invention relates to isolatedpolypeptides having at least 60%, e.g., at least 65%, at least 70%, atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO:26; at least 65%, e.g., at least 70%, at least 75%, at least 80%, atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 28; at least 70%, e.g., atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 30or SEQ ID NO: 32; at least 80%, e.g., at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 34, SEQ ID NO: 36, or SEQ ID NO: 38; at least 85%, e.g., atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 40 or SEQ ID NO: 42; at least97%, e.g., at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 44; or at least 98%, e.g., at least 99% or100% sequence identity to the polypeptide of SEQ ID NO: 46, which haveendoglucanase activity. In one aspect, the polypeptides differ by up to10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, from thepolypeptide of SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO:32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ IDNO: 42, SEQ ID NO: 44, or SEQ ID NO: 46.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 26; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 26.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 28; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 28.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 30; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 30.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 32; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 32.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 34; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 34.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 36; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 36.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 38; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 38.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 40; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 40.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 42; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 42.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 44; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 44.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 46; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 46.

In another embodiment, the present invention relates to isolatedpolypeptides having at least 70%, e.g., at least 75%, at least 80%, atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 48; at least 75%, e.g., atleast 80%, at least 81%, at least 82%, at least 83%, at least 84%, atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide of SEQ ID NO: 50, SEQ ID NO:52, SEQ ID NO: 54, or SEQ ID NO: 79; at least 80%, e.g., at least 81%,at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO:62, or SEQ ID NO: 64; at least 85%, e.g., at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 66; or at least 90%, e.g., at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 68, SEQ ID NO: 70, or SEQ ID NO: 72, which have cellulolyticenhancing activity. In one aspect, the polypeptides differ by up to 10amino acids, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, from thepolypeptide of SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO:54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ IDNO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, orSEQ ID NO: 79.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 48; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 48.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 50; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 50.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 52; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 52.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 54; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 54.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 56; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 56.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 58; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 58.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 60; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 60.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 62; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 62.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 64; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 64.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 66; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 66.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 68; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 68.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 70; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 70.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 72; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 72.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 79; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 79.

In another embodiment, the present invention relates to isolatedpolypeptides having at least 70%, e.g., at least 75%, at least 80%, atleast 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 74, at least 94%, e.g., atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide of SEQ ID NO: 78, or at least98%, e.g., at least 99% or 100% sequence identity to the polypeptide ofSEQ ID NO: 76, which have xylanase activity. In one aspect, thepolypeptides differ by up to 10 amino acids, e.g., 1, 2, 3, 4, 5, 6, 7,8, 9, or 10, from the polypeptide of SEQ ID NO: 74, SEQ ID NO: 76, orSEQ ID NO: 78.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 74; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 74.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 76; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 76.

A polypeptide of the present invention preferably comprises or consistsof the amino acid sequence of SEQ ID NO: 78; or an allelic variantthereof; or is a fragment thereof having cellobiohydrolase activity. Inanother aspect, the polypeptide comprises or consists of the polypeptideof SEQ ID NO: 78.

In another embodiment, the present invention relates to isolatedpolypeptides having cellobiohydrolase activity encoded bypolynucleotides that hybridize under very low stringency conditions, lowstringency conditions, medium stringency conditions, medium-highstringency conditions, high stringency conditions, or very highstringency conditions with (i) the polypeptide coding sequence of SEQ IDNO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, or SEQ ID NO: 9, (ii)the cDNA sequence thereof, or (iii) the full-length complement of (i) or(ii) (Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2ndedition, Cold Spring Harbor, N.Y.).

In another embodiment, the present invention relates to isolatedpolypeptides having cellobiohydrolase activity encoded bypolynucleotides that hybridize under very low stringency conditions, lowstringency conditions, medium stringency conditions, medium-highstringency conditions, high stringency conditions, or very highstringency conditions with (i) the polypeptide coding sequence of SEQ IDNO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQID NO: 21, or SEQ ID NO: 23, (ii) the cDNA sequence thereof, or (iii)the full-length complement of (i) or (ii) (Sambrook et al., 1989,Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor,N.Y.).

In another embodiment, the present invention relates to isolatedpolypeptides having endoglucanase activity encoded by polynucleotidesthat hybridize under very low stringency conditions, low stringencyconditions, medium stringency conditions, medium-high stringencyconditions, high stringency conditions, or very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 25,SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO:35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, or SEQID NO: 45, (ii) the cDNA sequence thereof, or (iii) the full-lengthcomplement of (i) or (ii) (Sambrook et al., 1989, Molecular Cloning, ALaboratory Manual, 2d edition, Cold Spring Harbor, N.Y.).

In another embodiment, the present invention relates to isolatedpolypeptides having cellulolytic enhancing activity encoded bypolynucleotides that hybridize under very low stringency conditions, lowstringency conditions, medium stringency conditions, medium-highstringency conditions, high stringency conditions, or very highstringency conditions with (i) the polypeptide coding sequence of SEQ IDNO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65,SEQ ID NO: 67, SEQ ID NO: 69, or SEQ ID NO: 71, (ii) the cDNA sequencethereof, or (iii) the full-length complement of (i) or (ii) (Sambrook etal., 1989, Molecular Cloning, A Laboratory Manual, 2d edition, ColdSpring Harbor, N.Y.).

In another embodiment, the present invention relates to isolatedpolypeptides having xylanase activity encoded by polynucleotides thathybridize under very low stringency conditions, low stringencyconditions, medium stringency conditions, medium-high stringencyconditions, high stringency conditions, or very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 73,SEQ ID NO: 75, or SEQ ID NO: 77, (ii) the cDNA sequence thereof, or(iii) the full-length complement of (i) or (ii) (Sambrook et al., 1989,Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor,N.Y.).

The polynucleotide of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ IDNO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ IDNO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35,SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO:45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ IDNO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73,SEQ ID NO: 75, or SEQ ID NO: 77, or a subsequence thereof, as well asthe polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36,SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO:46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ IDNO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 74, SEQ ID NO: 76,SEQ ID NO: 78, or SEQ ID NO: 79, the mature polypeptide thereof, or afragment thereof, may be used to design nucleic acid probes to identifyand clone DNA encoding polypeptides having cellobiohydrolase,endoglucanase, cellulolytic enhancing, or xylanase activity from strainsof different genera or species according to methods well known in theart. In particular, such probes can be used for hybridization with thegenomic DNA or cDNA of a cell of interest, following standard Southernblotting procedures, in order to identify and isolate the correspondinggene therein. Such probes can be considerably shorter than the entiresequence, but should be at least 15, e.g., at least 25, at least 35, orat least 70 nucleotides in length. Preferably, the nucleic acid probe isat least 100 nucleotides in length, e.g., at least 200 nucleotides, atleast 300 nucleotides, at least 400 nucleotides, at least 500nucleotides, at least 600 nucleotides, at least 700 nucleotides, atleast 800 nucleotides, or at least 900 nucleotides in length. Both DNAand RNA probes can be used. The probes are typically labeled fordetecting the corresponding gene (for example, with ³²P, ³H, ³⁵S,biotin, or avidin). Such probes are encompassed by the presentinvention.

A genomic DNA or cDNA library prepared from such other strains may bescreened for DNA that hybridizes with the probes described above andencodes a polypeptide having cellobiohydrolase, endoglucanase,cellulolytic enhancing, or xylanase activity. Genomic or other DNA fromsuch other strains may be separated by agarose or polyacrylamide gelelectrophoresis, or other separation techniques. DNA from the librariesor the separated DNA may be transferred to and immobilized onnitrocellulose or other suitable carrier material. In order to identifya clone or DNA that hybridizes with SEQ ID NO: 1, SEQ ID NO: 3, SEQ IDNO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ IDNO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33,SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO:43, SEQ ID NO: 45. SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ IDNO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71,SEQ ID NO: 73, SEQ ID NO: 75, or SEQ ID NO: 77, the mature polypeptidecoding sequence thereof, or a subsequence thereof, the carrier materialis used in a Southern blot.

For purposes of the present invention, hybridization indicates that thepolynucleotides hybridize to a labeled nucleic acid probe correspondingto (i) SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ IDNO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27,SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO:37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ IDNO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65,SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO:75, or SEQ ID NO: 77; (ii) the polypeptide coding sequence thereof;(iii) the cDNA sequence thereof; (iv) the full-length complementthereof; or (v) a subsequence thereof; under very low to very highstringency conditions. Molecules to which the nucleic acid probehybridizes under these conditions can be detected using, for example,X-ray film or any other detection means known in the art.

In one aspect, the nucleic acid probe is a polynucleotide that encodesthe polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ IDNO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36,SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, SEQ ID NO:46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ IDNO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 74, SEQ ID NO: 76,SEQ ID NO: 78, or SEQ ID NO: 79; the mature polypeptide thereof; or afragment thereof. In another aspect, the nucleic acid probe is SEQ IDNO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ IDNO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29,SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO:39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ IDNO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67,SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, or SEQ IDNO: 77; the mature polypeptide coding sequence thereof; or the cDNAsequence thereof.

In another embodiment, the present invention relates to isolatedpolypeptides having cellobiohydrolase activity encoded bypolynucleotides having at least 80%, e.g., at least 81%, at least 82%,at least 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 1 or SEQ ID NO: 3, or the cDNA sequencesthereof; at least 90%, e.g., at least 91%, at least 92%, at least 93%,at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 5 or the cDNA sequence thereof; at least 91%, e.g., atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 7 or the cDNA sequencesthereof; or at least 99%, e.g., 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 9 or the cDNA sequencethereof.

In another embodiment, the present invention relates to isolatedpolypeptides having cellobiohydrolase activity encoded bypolynucleotides having at least 70%, e.g., at least 75%, at least 80%,at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence SEQ ID NO: 11 or the cDNAsequence thereof; at least 80%, e.g., at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 13 or SEQ ID NO: 15, or the cDNA sequencesthereof; at least 91%, e.g., at least 92%, at least 93%, at least 94%,at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:17 or the cDNA sequence thereof; at least 96%, e.g., at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 19 or the cDNA sequence thereof; or atleast 98%, e.g., at least 99% or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 21 or SEQ ID NO: 23, or thecDNA sequences thereof.

In another embodiment, the present invention relates to isolatedpolypeptides having endoglucanase activity encoded by polynucleotideshaving at least 60%, e.g., at least 65%, at least 70%, at least 75%, atleast 80%, at least 81%, at least 82%, at least 83%, at least 84%, atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:25 or the cDNA sequence thereof; at least 65%, e.g., at least 70%, atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 27 or the cDNA sequence thereof; at least 70%, e.g., atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 29 or SEQ ID NO: 31, or the cDNA sequences thereof; atleast 80%, e.g., at least 81%, at least 82%, at least 83%, at least 84%,at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:33, SEQ ID NO: 35, or SEQ ID NO: 37, or the cDNA sequences thereof; atleast 85%, e.g., at least 86%, at least 87%, at least 88%, at least 89%,at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:39 or SEQ ID NO: 41, or the cDNA sequences thereof; at least 97%, e.g.,at least 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 43 or the cDNA sequence thereof; or atleast 98%, e.g., at least 99% or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 45 or the cDNA sequencethereof.

In another embodiment, the present invention relates to isolatedpolypeptides having cellulolytic enhancing activity encoded bypolynucleotides having at least 70%, e.g., at least 75%, at least 80%,at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 47 or the cDNAsequence thereof; at least 75%, e.g., at least 80%, at least 81%, atleast 82%, at least 83%, at least 84%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 49, SEQ ID NO: 51, or SEQ IDNO: 53, or the cDNA sequences thereof; at least 80%, e.g., at least 81%,at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO:59, SEQ ID NO: 61, or SEQ ID NO: 63, or the cDNA sequences thereof; atleast 85%, e.g., at least 86%, at least 87%, at least 88%, at least 89%,at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:65 or the cDNA sequence thereof; or at least 90%, e.g., at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 67, SEQ ID NO: 69, or SEQ IDNO: 71, or the cDNA sequences thereof.

In another embodiment, the present invention relates to isolatedpolypeptides having xylanase activity encoded by polynucleotides havingat least 70%, e.g., at least 75%, at least 80%, at least 81%, at least82%, at least 83%, at least 84%, at least 85%, at least 86%, at least87%, at least 88%, at least 89%, at least 90%, at least 91%, at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 73 or the cDNA sequencethereof, at least 94%, e.g., at least 95%, at least 96%, at least 97%,at least 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 77 or the cDNA sequence thereof, or atleast 98%, e.g., at least 99% or 100% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 75 or the cDNA sequencethereof.

In another embodiment, the present invention relates to variantscomprising the polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6,SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO: 24, SEQ IDNO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44,SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO:54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ IDNO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 74, SEQID NO: 76, SEQ ID NO: 78, or SEQ ID NO: 79 comprising a substitution,deletion, and/or insertion at one or more (e.g., several) positions. Inan embodiment, the number of amino acid substitutions, deletions and/orinsertions introduced into the polypeptide of SEQ ID NO: 2, SEQ ID NO:4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO:14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ IDNO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42,SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO:52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ IDNO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, or SEQ ID NO: 79 is up to 10,e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10. The amino acid changes may be ofa minor nature, that is conservative amino acid substitutions orinsertions that do not significantly affect the folding and/or activityof the protein; small deletions, typically of 1-30 amino acids; smallamino- or carboxyl-terminal extensions, such as an amino-terminalmethionine residue; a small linker peptide of up to 20-25 residues; or asmall extension that facilitates purification by changing net charge oranother function, such as a poly-histidine tract, an antigenic epitopeor a binding domain.

Examples of conservative substitutions are within the groups of basicamino acids (arginine, lysine and histidine), acidic amino acids(glutamic acid and aspartic acid), polar amino acids (glutamine andasparagine), hydrophobic amino acids (leucine, isoleucine and valine),aromatic amino acids (phenylalanine, tryptophan and tyrosine), and smallamino acids (glycine, alanine, serine, threonine and methionine). Aminoacid substitutions that do not generally alter specific activity areknown in the art and are described, for example, by H. Neurath and R. L.Hill, 1979, In, The Proteins, Academic Press, New York. Commonsubstitutions are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly, Ala/Thr,Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile,Leu/Val, Ala/Glu, and Asp/Gly.

Alternatively, the amino acid changes are of such a nature that thephysico-chemical properties of the polypeptides are altered. Forexample, amino acid changes may improve the thermal stability of thepolypeptide, alter the substrate specificity, change the pH optimum, orthe like.

Essential amino acids in a polypeptide can be identified according toprocedures known in the art, such as site-directed mutagenesis oralanine-scanning mutagenesis (Cunningham and Wells, 1989, Science 244:1081-1085). In the latter technique, single alanine mutations areintroduced at every residue in the molecule, and the resultant mutantmolecules are tested for cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity to identify amino acid residues that arecritical to the activity of the molecule. See also, Hilton et al., 1996,J. Biol. Chem. 271: 4699-4708. The active site of the enzyme or otherbiological interaction can also be determined by physical analysis ofstructure, as determined by such techniques as nuclear magneticresonance, crystallography, electron diffraction, or photoaffinitylabeling, in conjunction with mutation of putative contact site aminoacids. See, for example, de Vos et al., 1992, Science 255: 306-312;Smith et al., 1992, J. Mol. Biol. 224: 899-904; Wlodaver et al., 1992,FEBS Lett. 309: 59-64. The identity of essential amino acids can also beinferred from an alignment with a related polypeptide.

Single or multiple amino acid substitutions, deletions, and/orinsertions can be made and tested using known methods of mutagenesis,recombination, and/or shuffling, followed by a relevant screeningprocedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988,Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can beused include error-prone PCR, phage display (e.g., Lowman et al., 1991,Biochemistry 30: 10832-10837; U.S. Pat. No. 5,223,409; WO 92/06204), andregion-directed mutagenesis (Derbyshire et al., 1986, Gene 46: 145; Neret al., 1988, DNA 7: 127).

Mutagenesis/shuffling methods can be combined with high-throughput,automated screening methods to detect activity of cloned, mutagenizedpolypeptides expressed by host cells (Ness et al., 1999, NatureBiotechnology 17: 893-896). Mutagenized DNA molecules that encode activepolypeptides can be recovered from the host cells and rapidly sequencedusing standard methods in the art. These methods allow the rapiddetermination of the importance of individual amino acid residues in apolypeptide.

A polypeptide of the present invention may be a hybrid polypeptide inwhich a region of one polypeptide is fused at the N-terminus or theC-terminus of a region of another polypeptide.

A polypeptide of the present invention may be a fusion polypeptide orcleavable fusion polypeptide in which another polypeptide is fused atthe N-terminus or the C-terminus of the polypeptide of the presentinvention. A fusion polypeptide is produced by fusing a polynucleotideencoding another polypeptide to a polynucleotide of the presentinvention. Techniques for producing fusion polypeptides are known in theart, and include ligating the coding sequences encoding the polypeptidesso that they are in frame and that expression of the fusion polypeptideis under control of the same promoter(s) and terminator. Fusionpolypeptides may also be constructed using intein technology in whichfusion polypeptides are created post-translationally (Cooper et al.,1993, EMBO J. 12: 2575-2583; Dawson et al., 1994, Science 266: 776-779).

A fusion polypeptide can further comprise a cleavage site between thetwo polypeptides. Upon secretion of the fusion protein, the site iscleaved releasing the two polypeptides. Examples of cleavage sitesinclude, but are not limited to, the sites disclosed in Martin et al.,2003, J. Ind. Microbiol. Biotechnol. 3: 568-576; Svetina et al., 2000,J. Biotechnol. 76: 245-251; Rasmussen-Wilson et al., 1997, Appl.Environ. Microbiol. 63: 3488-3493; Ward et al., 1995, Biotechnology 13:498-503; and Contreras et al., 1991, Biotechnology 9: 378-381; Eaton etal., 1986, Biochemistry 25: 505-512; Collins-Racie et al., 1995,Biotechnology 13: 982-987; Carter et al., 1989, Proteins: Structure,Function, and Genetics 6: 240-248; and Stevens, 2003, Drug DiscoveryWorld 4: 35-48.

In one embodiment, a cellulose-degrading polypeptide of the presentinvention may be functionally stable over a temperature of up to 120°C., in particular up to 100° C. in particular up to 80° C., inparticular up to 70° C., in particular up to 60° C. more particularly upto 50° C.

In another embodiment, a cellulose-degrading polypeptide of the presentinvention may exhibit optimum substrate hydrolysis or substratehydrolysis enhancing activity at a temperature within the range fromabout 10° C. to about 90° C., such as about 10° C. to about 80° C.,particularly in the range from about 20° C. to about 60° C. or about 50°C. to about 80° C.

In another embodiment, a cellulose-degrading polypeptide of the presentinvention may exhibit optimum substrate hydrolysis or substratehydrolysis enhancing activity at a pH within the range from about pH 2to about 10, such as about 3 to about 9, particularly in the range fromabout 4 to about 8 or about 5 to about 7.

In another embodiment, a cellulose-degrading polypeptide of the presentinvention enhances the hydrolysis of a cellulosic material incombination with other enzymes having cellulolytic activity.

Sources of Polypeptides Having Cellulolytic or Hemicellulolytic Activity

A polypeptide having cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity of the present invention may be obtainedfrom microorganisms of any genus. For purposes of the present invention,the term “obtained from” as used herein in connection with a givensource shall mean that the polypeptide encoded by a polynucleotide isproduced by the source or by a strain in which the polynucleotide fromthe source has been inserted. In one aspect, the polypeptide obtainedfrom a given source is secreted extracellularly. In another aspect, thepolypeptide may be obtained from a microorganism such as a prokaryoticcell, an archaeal cell or a eukaryotic cell. In another aspect, thepolypeptide may be synthetically made, naturally occurring, or acombination thereof.

In another aspect, the polypeptide is a Chaetomium polypeptide. Inanother aspect, the polypeptide is a Chaetomium senegalense polypeptide.In another aspect, the polypeptide is a Chaetomium thermophilumpolypeptide.

In another aspect, the polypeptide is a Corynascus polypeptide. Inanother aspect, the polypeptide is a Corynascus thermophiluspolypeptide.

In another aspect, the polypeptide is a Maibranchea polypeptide. Inanother aspect, the polypeptide is a Maibranchea cinnamomea polypeptide.

In another aspect, the polypeptide is a Melanocarpus polypeptide. Inanother aspect, the polypeptide is a Melanocarpus albomyces polypeptide.

In another aspect, the polypeptide is a Remersonia polypeptide. Inanother aspect, the polypeptide is a Remersonia thermophila polypeptide.

In another aspect, the polypeptide is a Rhizomucor polypeptide. Inanother aspect, the polypeptide is a Rhizomucor miehei polypeptide.

In another aspect, the polypeptide is a Scytalidium polypeptide. Inanother aspect, the polypeptide is a Scytalidium indonesiacumpolypeptide.

In another aspect, the polypeptide is a Talaromyces polypeptide. Inanother aspect, the polypeptide is a Talaromyces byssochiamydoidespolypeptide. In another aspect, the polypeptide is a Talaromycesemersonii polypeptide. In another aspect, the polypeptide is aTalaromyces leycettanus polypeptide. In another aspect, the polypeptideis a Talaromyces thermophilus polypeptide.

In another aspect, the polypeptide is a Thermoascus polypeptide. Inanother aspect, the polypeptide is a Thermoascus aurantiacuspolypeptide.

In another aspect, the polypeptide is a Thermomyces polypeptide. Inanother aspect, the polypeptide is a Thermomyces lanuginosuspolypeptide.

In another aspect, the polypeptide is a Thermomucor polypeptide. Inanother aspect, the polypeptide is a Thermomucor indicae-seudaticaepolypeptide.

It will be understood that for the aforementioned species, the inventionencompasses both the perfect and imperfect states, and other taxonomicequivalents, e.g., anamorphs, regardless of the species name by whichthey are known. Those skilled in the art will readily recognize theidentity of appropriate equivalents.

Strains of these species are readily accessible to the public in anumber of culture collections, such as the American Type CultureCollection (ATCC), Deutsche Sammlung von Mikroorganismen andZellkulturen GmbH (DSMZ), Centraalbureau Voor Schimmelcultures (CBS),and Agricultural Research Service Patent Culture Collection, NorthernRegional Research Center (NRRL).

The polypeptide may be identified and obtained from other sourcesincluding microorganisms isolated from nature (e.g., soil, composts,water, etc.) or DNA samples obtained directly from natural materials(e.g., soil, composts, water, etc.) using the above-mentioned probes.Techniques for isolating microorganisms and DNA directly from naturalhabitats are well known in the art. A polynucleotide encoding thepolypeptide may then be obtained by similarly screening a genomic DNA orcDNA library of another microorganism or mixed DNA sample. Once apolynucleotide encoding a polypeptide has been detected with theprobe(s), the polynucleotide can be isolated or cloned by utilizingtechniques that are known to those of ordinary skill in the art (see,e.g., Sambrook et al., 1989, supra).

Polynucleotides

The present invention also relates to isolated polynucleotides encodinga polypeptide of the present invention, as described herein.

The techniques used to isolate or clone a polynucleotide are known inthe art and include isolation from genomic DNA or cDNA, or a combinationthereof. The cloning of the polynucleotides from genomic DNA can beeffected, e.g., by using the well known polymerase chain reaction (PCR)or antibody screening of expression libraries to detect cloned DNAfragments with shared structural features. See, e.g., Innis et al.,1990, PCR: A Guide to Methods and Application, Academic Press, New York.Other nucleic acid amplification procedures such as ligase chainreaction (LCR), ligation activated transcription (LAT) andpolynucleotide-based amplification (NASBA) may be used. Thepolynucleotides may be cloned from a strain of Chaetomium, Corynascus,Malbranchea, Melanocarpus, Remersonia, Scytalidium, Talaromyces,Thermomyces, or Thermomucor, or a related organism and thus, forexample, may be an allelic or species variant of the polypeptideencoding region of the polynucleotide.

Modification of a polynucleotide encoding a polypeptide of the presentinvention may be necessary for synthesizing polypeptides substantiallysimilar to the polypeptide. The term “substantially similar” to thepolypeptide refers to non-naturally occurring forms of the polypeptide.These polypeptides may differ in some engineered way from thepolypeptide isolated from its native source, e.g., variants that differin specific activity, thermostability, pH optimum, or the like. Thevariants may be constructed on the basis of the polynucleotide presentedas the polypeptide coding sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ IDNO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ IDNO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33,SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO:43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ IDNO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71,SEQ ID NO: 73, SEQ ID NO: 75, or SEQ ID NO: 77, or the cDNA sequencesthereof, by introduction of nucleotide substitutions that do not resultin a change in the amino acid sequence of the polypeptide, but whichcorrespond to the codon usage of the host organism intended forproduction of the enzyme, or by introduction of nucleotide substitutionsthat may give rise to a different amino acid sequence. For a generaldescription of nucleotide substitution, see, e.g., Ford et al., 1991,Protein Expression and Purification 2: 95-107.

In an embodiment, the polynucleotides of the present invention areselected from a DNA, cDNA, or RNA. The nucleotide sequence may beobtained by standard cloning procedures used in genetic engineering torelocate the nucleotide sequence from its natural location to adifferent site where it will be reproduced. The cloning procedures mayinvolve excision and isolation of a desired fragment comprising thenucleotide sequence encoding the polypeptide, insertion of the fragmentinto a vector molecule, and incorporation of the recombinant vector intoa host cell where multiple copies or clones of the nucleotide sequencewill be replicated. The nucleotide sequence may be of genomic, cDNA,RNA, semisynthetic, synthetic origin, or any combinations thereof.

In another embodiment, the polynucleotides of the present inventionbelong to the GH6, GH7, GH10, GH45 and GH61 families of glucosylhydrolases. In the present invention the nucleotide sequence wasobtained by generating libraries of known GH6, GH7, GH10, GH45 and GH61glucosyl hydrolases and running an algorithm that can identify conservedpeptide sequences, also called n-mers such as conserved hexapeptides.Such an algorithm includes the following steps: for each biopolymer makeall the n-mers that occur in the biopolymer sequence, select allbiopolymer that contain more than a defined number of the n-mers, makeall the n-mers that occur in these biopolymers and a defined number ofthe most abundant n-mers, go back to step 2 until no new n-mers are madein the following round. The algorithm is exemplified in Example 1 of thepresent invention and can for example be used to identify conservedpeptides in for example gene families or subgroup of gene families.

Practical testing has shown that a stretch of at least six conservedamino acids is necessary for design of functional primers for degeneratePCR from genomic DNA or cDNA (Sambrook and Russell, 2001, MolecularCloning: A Laboratory Manual, Third Edition, Cold Spring Harbor, N.Y.).On the other hand it can be difficult to find conserved amino acidsequences that are longer than six residues when working with large orvery divergent protein families. Therefore, a way to analyze a proteinfamily in order to find conserved peptides than can be used for designof degenerated primers is to identify the most frequently occurringhexapeptides in the family. Conserved hexapeptides were reversetranslated according to the genetic code and positions containing anynucleotide (A, C, G or T) were substituted with inosine. Degeneratenucleotides at the 3′ end of the primers were removed from the sequenceof the primers. The degeneracy of the primer that resulted from reversetranslation of each hexapeptide was calculated based on the genetic codeand substituting positions containing any nucleotide (A, C, G or T) withinosine. In addition, the relative position of the hexapeptides in theproteins was estimated as the median of the distance of the peptide tothe N-terminal of each protein in the subgroup that contained thepeptide.

Sequences for primers were selected based on three criteria: they shouldhave high frequency in the GH gene family, they should give an ampliconof at least 40 base pairs excluding primer sequences in order to obtainsufficient sequence information to identify the PCR product, and theprimers should have the smallest possible redundancy and redundant basesat the 3′ end are not allowed. A tail of six bases (CTGGAC) was added tothe 5′ end of all primer sequences as this improves the performance ofshort primers. Reverse primers were designed to be complementary to theDNA sequence encoding the hexapeptide and according to the same rulesand PCR from DNA of different microorganisms amplified and sequenceanalyzed. Detailed explanations of this approach are described herein inthe Examples of the present invention.

In another embodiment, a polynucleotide of the present invention may beisolated from or produced on the basis of a DNA library from aprokaryote, such as a bacterium or an eukaryote, such as a fungus oryeast.

In another embodiment, a polynucleotide of the present invention may beisolated from a fungus that degrades carbohydrates, such as cellulosicsubstrates. Such fungi include, e.g., Ascomycota, Basidiomycota,Zygomycota or Oomycota.

Nucleic Acid Constructs

The present invention also relates to nucleic acid constructs comprisinga polynucleotide of the present invention operably linked to one or more(e.g., several) control sequences that direct the expression of thecoding sequence in a suitable host cell under conditions compatible withthe control sequences.

A polynucleotide may be manipulated in a variety of ways to provide forexpression of the polypeptide. Manipulation of the polynucleotide priorto its insertion into a vector may be desirable or necessary dependingon the expression vector. The techniques for modifying polynucleotidesutilizing recombinant DNA methods are well known in the art.

The control sequence may be a promoter, a polynucleotide that isrecognized by a host cell for expression of a polynucleotide encoding apolypeptide of the present invention. The promoter containstranscriptional control sequences that mediate the expression of thepolypeptide. The promoter may be any polynucleotide that showstranscriptional activity in the host cell including mutant, truncated,and hybrid promoters, and may be obtained from genes encodingextracellular or intracellular polypeptides either homologous orheterologous to the host cell.

Examples of suitable promoters for directing transcription of thenucleic acid constructs of the present invention in a bacterial hostcell are the promoters obtained from the Bacillus amyloliquefaciensalpha-amylase gene (amyQ), Bacillus licheniformis alpha-amylase gene(amyL), Bacillus licheniformis penicillinase gene (penP), Bacillusstearothermophilus maltogenic amylase gene (amyM), Bacillus subtilislevansucrase gene (sacB), Bacillus subtilis xylA and xylB genes,Bacillus thuringiensis cryIIIA gene (Agaisse and Lereclus, 1994,Molecular Microbiology 13: 97-107), E. coli lac operon, E. coli trcpromoter (Egon et al., 1988, Gene 69: 301-315), Streptomyces coelicoloragarase gene (dagA), and prokaryotic beta-lactamase gene (Villa-Kamaroffet al., 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as thetac promoter (DeBoer et al., 1983, Proc. Natl. Acad. Sci. USA 80:21-25). Further promoters are described in “Useful proteins fromrecombinant bacteria” in Gilbert et al., 1980, Scientific American 242:74-94; and in Sambrook et al., 1989, supra. Examples of tandem promotersare disclosed in WO 99/43835.

Examples of suitable promoters for directing transcription of thenucleic acid constructs of the present invention in a filamentous fungalhost cell are promoters obtained from the genes for Aspergillus nidulansacetamidase, Aspergillus niger neutral alpha-amylase, Aspergillus nigeracid stable alpha-amylase, Aspergillus niger or Aspergillus awamoriglucoamylase (glaA), Aspergillus oryzae TAKA amylase, Aspergillus oryzaealkaline protease, Aspergillus oryzae triose phosphate isomerase,Fusarium oxysporum trypsin-like protease (WO 96/00787), Fusariumvenenatum amyloglucosidase (WO 00/56900), Fusarium venenatum Daria (WO00/56900), Fusarium venenatum Quinn (WO 00/56900), Rhizomucor mieheilipase, Rhizomucor miehei aspartic proteinase, Trichoderma reeseibeta-glucosidase, Trichoderma reesei cellobiohydrolase I, Trichodermareesei cellobiohydrolase II, Trichoderma reesei endoglucanase I,Trichoderma reesei endoglucanase II, Trichoderma reesei endoglucanaseIII, Trichoderma reesei endoglucanase V, Trichoderma reesei xylanase I,Trichoderma reesei xylanase II, Trichoderma reesei xylanase III,Trichoderma reesei beta-xylosidase, and Trichoderma reesei translationelongation factor, as well as the NA2-tpi promoter (a modified promoterfrom an Aspergillus neutral alpha-amylase gene in which the untranslatedleader has been replaced by an untranslated leader from an Aspergillustriose phosphate isomerase gene; non-limiting examples include modifiedpromoters from an Aspergillus niger neutral alpha-amylase gene in whichthe untranslated leader has been replaced by an untranslated leader froman Aspergillus nidulans or Aspergillus oryzae triose phosphate isomerasegene); and mutant, truncated, and hybrid promoters thereof. Otherpromoters are described in U.S. Pat. No. 6,011,147.

In a yeast host, useful promoters are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiaegalactokinase (GAL1), Saccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP),Saccharomyces cerevisiae triose phosphate isomerase (TPI), Saccharomycescerevisiae metallothionein (CUP1), and Saccharomyces cerevisiae3-phosphoglycerate kinase. Other useful promoters for yeast host cellsare described by Romanos et al., 1992, Yeast 8: 423-488.

The control sequence may also be a transcription terminator, which isrecognized by a host cell to terminate transcription. The terminator isoperably linked to the 3′-terminus of the polynucleotide encoding thepolypeptide. Any terminator that is functional in the host cell may beused in the present invention.

Preferred terminators for bacterial host cells are obtained from thegenes for Bacillus clausii alkaline protease (aprH), Bacilluslicheniformis alpha-amylase (amyL), and Escherichia coli ribosomal RNA(rrnB).

Preferred terminators for filamentous fungal host cells are obtainedfrom the genes for Aspergillus nidulans acetamidase, Aspergillusnidulans anthranilate synthase, Aspergillus niger glucoamylase,Aspergillus niger alpha-glucosidase, Aspergillus oryzae TAKA amylase,Fusarium oxysporum trypsin-like protease, Trichoderma reeseibeta-glucosidase, Trichoderma reesei cellobiohydrolase I, Trichodermareesei cellobiohydrolase II, Trichoderma reesei endoglucanase I,Trichoderma reesei endoglucanase II, Trichoderma reesei endoglucanaseIII, Trichoderma reesei endoglucanase V, Trichoderma reesei xylanase I,Trichoderma reesei xylanase II, Trichoderma reesei xylanase III,Trichoderma reesei beta-xylosidase, and Trichoderma reesei translationelongation factor.

Preferred terminators for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae enolase, Saccharomyces cerevisiaecytochrome C (CYC1), and Saccharomyces cerevisiaeglyceraldehyde-3-phosphate dehydrogenase. Other useful terminators foryeast host cells are described by Romanos et al., 1992, supra.

The control sequence may also be an mRNA stabilizer region downstream ofa promoter and upstream of the coding sequence of a gene which increasesexpression of the gene.

Examples of suitable mRNA stabilizer regions are obtained from aBacillus thuringiensis cryIIIA gene (WO 94/25612) and a Bacillussubtilis SP82 gene (Hue et al., 1995, Journal of Bacteriology 177:3465-3471).

The control sequence may also be a leader, a nontranslated region of anmRNA that is important for translation by the host cell. The leader isoperably linked to the 5′-terminus of the polynucleotide encoding thepolypeptide. Any leader that is functional in the host cell may be used.

Preferred leaders for filamentous fungal host cells are obtained fromthe genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulanstriose phosphate isomerase.

Suitable leaders for yeast host cells are obtained from the genes forSaccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, andSaccharomyces cerevisiae alcoholdehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequenceoperably linked to the 3′-terminus of the polynucleotide and, whentranscribed, is recognized by the host cell as a signal to addpolyadenosine residues to transcribed mRNA. Any polyadenylation sequencethat is functional in the host cell may be used.

Preferred polyadenylation sequences for filamentous fungal host cellsare obtained from the genes for Aspergillus nidulans anthranilatesynthase, Aspergillus niger glucoamylase, Aspergillus nigeralpha-glucosidase Aspergillus oryzae TAKA amylase, and Fusariumoxysporum trypsin-like protease.

Useful polyadenylation sequences for yeast host cells are described byGuo and Sherman, 1995, Mol. Cellular Biol. 15: 5983-5990.

The control sequence may also be a signal peptide coding region thatencodes a signal peptide linked to the N-terminus of a polypeptide anddirects the polypeptide into the cell's secretory pathway. The 5′-end ofthe coding sequence of the polynucleotide may inherently contain asignal peptide coding sequence naturally linked in translation readingframe with the segment of the coding sequence that encodes thepolypeptide. Alternatively, the 5′-end of the coding sequence maycontain a signal peptide coding sequence that is foreign to the codingsequence. A foreign signal peptide coding sequence may be required wherethe coding sequence does not naturally contain a signal peptide codingsequence. Alternatively, a foreign signal peptide coding sequence maysimply replace the natural signal peptide coding sequence in order toenhance secretion of the polypeptide. However, any signal peptide codingsequence that directs the expressed polypeptide into the secretorypathway of a host cell may be used.

Effective signal peptide coding sequences for bacterial host cells arethe signal peptide coding sequences obtained from the genes for BacillusNCI B 11837 maltogenic amylase, Bacillus licheniformis subtilisin,Bacillus licheniformis beta-lactamase, Bacillus stearothermophilusalpha-amylase, Bacillus stearothermophilus neutral proteases (nprT,nprS, nprM), and Bacillus subtilis prsA. Further signal peptides aredescribed by Simonen and Palva, 1993, Microbiological Reviews 57:109-137.

Effective signal peptide coding sequences for filamentous fungal hostcells are the signal peptide coding sequences obtained from the genesfor Aspergillus niger neutral amylase, Aspergillus niger glucoamylase,Aspergillus oryzae TAKA amylase, Humicola insolens cellulase, Humicolainsolens endoglucanase V, Humicola lanuginosa lipase, and Rhizomucormiehei aspartic proteinase.

Useful signal peptides for yeast host cells are obtained from the genesfor Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiaeinvertase. Other useful signal peptide coding sequences are described byRomanos et al., 1992, supra.

The control sequence may also be a propeptide coding sequence thatencodes a propeptide positioned at the N-terminus of a polypeptide. Theresultant polypeptide is known as a proenzyme or propolypeptide (or azymogen in some cases). A propolypeptide is generally inactive and canbe converted to an active polypeptide by catalytic or autocatalyticcleavage of the propeptide from the propolypeptide. The propeptidecoding sequence may be obtained from the genes for Bacillus subtilisalkaline protease (aprE), Bacillus subtilis neutral protease (nprT),Myceliophthora thermophila laccase (WO 95/33836), Rhizomucor mieheiaspartic proteinase, and Saccharomyces cerevisiae alpha-factor.

Where both signal peptide and propeptide sequences are present, thepropeptide sequence is positioned next to the N-terminus of apolypeptide and the signal peptide sequence is positioned next to theN-terminus of the propeptide sequence.

It may also be desirable to add regulatory sequences that regulateexpression of the polypeptide relative to the growth of the host cell.Examples of regulatory sequences are those that cause expression of thegene to be turned on or off in response to a chemical or physicalstimulus, including the presence of a regulatory compound. Regulatorysequences in prokaryotic systems include the lac, tac, and trp operatorsystems. In yeast, the ADH2 system or GAL1 system may be used. Infilamentous fungi, the Aspergillus niger glucoamylase promoter,Aspergillus oryzae TAKA alpha-amylase promoter, and Aspergillus oryzaeglucoamylase promoter, Trichoderma reesei cellobiohydrolase I promoter,and Trichoderma reesei cellobiohydrolase II promoter may be used. Otherexamples of regulatory sequences are those that allow for geneamplification. In eukaryotic systems, these regulatory sequences includethe dihydrofolate reductase gene that is amplified in the presence ofmethotrexate, and the metallothionein genes that are amplified withheavy metals. In these cases, the polynucleotide encoding thepolypeptide would be operably linked to the regulatory sequence.

Expression Vectors

The present invention also relates to recombinant expression vectorscomprising a polynucleotide of the present invention, a promoter, andtranscriptional and translational stop signals. The various nucleotideand control sequences may be joined together to produce a recombinantexpression vector that may include one or more (e.g., several)convenient restriction sites to allow for insertion or substitution ofthe polynucleotide encoding the polypeptide at such sites.Alternatively, the polynucleotide may be expressed by inserting thepolynucleotide or a nucleic acid construct comprising the polynucleotideinto an appropriate vector for expression. In creating the expressionvector, the coding sequence is located in the vector so that the codingsequence is operably linked with the appropriate control sequences forexpression.

The recombinant expression vector may be any vector (e.g., a plasmid orvirus) that can be conveniently subjected to recombinant DNA proceduresand can bring about expression of the polynucleotide. The choice of thevector will typically depend on the compatibility of the vector with thehost cell into which the vector is to be introduced. The vector may be alinear or closed circular plasmid.

The vector may be an autonomously replicating vector, i.e., a vectorthat exists as an extrachromosomal entity, the replication of which isindependent of chromosomal replication, e.g., a plasmid, anextrachromosomal element, a minichromosome, or an artificial chromosome.The vector may contain any means for assuring self-replication.Alternatively, the vector may be one that, when introduced into the hostcell, is integrated into the genome and replicated together with thechromosome(s) into which it has been integrated. Furthermore, a singlevector or plasmid or two or more vectors or plasmids that togethercontain the total DNA to be introduced into the genome of the host cell,or a transposon, may be used.

The vector preferably contains one or more (e.g., several) selectablemarkers that permit easy selection of transformed, transfected,transduced, or the like cells. A selectable marker is a gene the productof which provides for biocide or viral resistance, resistance to heavymetals, prototrophy to auxotrophs, and the like.

Examples of bacterial selectable markers are Bacillus licheniformis orBacillus subtilis dal genes, or markers that confer antibioticresistance such as ampicillin, chloramphenicol, kanamycin, neomycin,spectinomycin, or tetracycline resistance. Suitable markers for yeasthost cells include, but are not limited to, ADE2, HIS3, LEU2, LYS2,MET3, TRP1, and URA3. Selectable markers for use in a filamentous fungalhost cell include, but are not limited to, adeA(phosphoribosylaminoimidazole-succinocarboxamide synthase), adeB(phosphoribosyl-aminoimidazole synthase), amdS (acetamidase), argB(ornithine carbamoyltransferase), bar (phosphinothricinacetyltransferase), hph (hygromycin phosphotransferase), niaD (nitratereductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfateadenyltransferase), and trpC (anthranilate synthase), as well asequivalents thereof. Preferred for use in an Aspergillus cell areAspergillus nidulans or Aspergillus oryzae amdS and pyrG genes and aStreptomyces hygroscopicus bargene. Preferred for use in a Trichodermacell are adeA, adeB, amdS, hph, and pyrG genes.

The selectable marker may be a dual selectable marker system asdescribed in WO 2010/039889. In one aspect, the dual selectable markeris a hph-tk dual selectable marker system.

The vector preferably contains an element(s) that permits integration ofthe vector into the host cell's genome or autonomous replication of thevector in the cell independent of the genome.

For integration into the host cell genome, the vector may rely on thepolynucleotide's sequence encoding the polypeptide or any other elementof the vector for integration into the genome by homologous ornon-homologous recombination. Alternatively, the vector may containadditional polynucleotides for directing integration by homologousrecombination into the genome of the host cell at a precise location(s)in the chromosome(s). To increase the likelihood of integration at aprecise location, the integrational elements should contain a sufficientnumber of nucleic acids, such as 100 to 10,000 base pairs, 400 to 10,000base pairs, and 800 to 10,000 base pairs, which have a high degree ofsequence identity to the corresponding target sequence to enhance theprobability of homologous recombination. The integrational elements maybe any sequence that is homologous with the target sequence in thegenome of the host cell. Furthermore, the integrational elements may benon-encoding or encoding polynucleotides. On the other hand, the vectormay be integrated into the genome of the host cell by non-homologousrecombination.

For autonomous replication, the vector may further comprise an origin ofreplication enabling the vector to replicate autonomously in the hostcell in question. The origin of replication may be any plasmidreplicator mediating autonomous replication that functions in a cell.The term “origin of replication” or “plasmid replicator” means apolynucleotide that enables a plasmid or vector to replicate in vivo.

Examples of bacterial origins of replication are the origins ofreplication of plasmids pBR322, pUC19, pACYC177, and pACYC184 permittingreplication in E. coli, and pUB110, pE194, pTA1060, and pAM111permitting replication in Bacillus.

Examples of origins of replication for use in a yeast host cell are the2 micron origin of replication, ARS1, ARS4, the combination of ARS1 andCEN3, and the combination of ARS4 and CEN6.

Examples of origins of replication useful in a filamentous fungal cellare AMA1 and ANSI (Gems et al., 1991, Gene 98: 61-67; Cullen et al.,1987, Nucleic Acids Res. 15: 9163-9175; WO 00/24883). Isolation of theAMA1 gene and construction of plasmids or vectors comprising the genecan be accomplished according to the methods disclosed in WO 00/24883.

More than one copy of a polynucleotide of the present invention may beinserted into a host cell to increase production of a polypeptide. Anincrease in the copy number of the polynucleotide can be obtained byintegrating at least one additional copy of the sequence into the hostcell genome or by including an amplifiable selectable marker gene withthe polynucleotide where cells containing amplified copies of theselectable marker gene, and thereby additional copies of thepolynucleotide, can be selected for by cultivating the cells in thepresence of the appropriate selectable agent.

The procedures used to ligate the elements described above to constructthe recombinant expression vectors of the present invention are wellknown to one skilled in the art (see, e.g., Sambrook et al., 1989,supra).

Host Cells

The present invention also relates to recombinant host cells, comprisinga polynucleotide of the present invention operably linked to one or more(e.g., several) control sequences that direct the production of apolypeptide of the present invention. A construct or vector comprising apolynucleotide is introduced into a host cell so that the construct orvector is maintained as a chromosomal integrant or as a self-replicatingextra-chromosomal vector as described earlier. The term “host cell”encompasses any progeny of a parent cell that is not identical to theparent cell due to mutations that occur during replication. The choiceof a host cell will to a large extent depend upon the gene encoding thepolypeptide and its source.

The host cell may be any cell useful in the recombinant production of apolypeptide of the present invention, e.g., a prokaryote or a eukaryote.

The prokaryotic host cell may be any Gram-positive or Gram-negativebacterium. Gram-positive bacteria include, but are not limited to,Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus,Lactococcus, Oceanobacillus, Staphylococcus, Streptococcus, andStreptomyces. Gram-negative bacteria include, but are not limited to,Campylobacter, E. coli, Flavobacterium, Fusobacterium, Helicobacter,Ilyobacter, Neisseria, Pseudomonas, Salmonella, and Ureaplasma.

The bacterial host cell may be any Bacillus cell including, but notlimited to, Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillusbrevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans,Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacilluslicheniformis, Bacillus megaterium, Bacillus pumilus, Bacillusstearothermophilus, Bacillus subtilis, and Bacillus thuringiensis cells.

The bacterial host cell may also be any Streptococcus cell including,but not limited to, Streptococcus equisimilis, Streptococcus pyogenes,Streptococcus uberis, and Streptococcus equi subsp. Zooepidemicus cells.

The bacterial host cell may also be any Streptomyces cell including, butnot limited to, Streptomyces achromogenes, Streptomyces avermitilis,Streptomyces coelicolor, Streptomyces griseus, and Streptomyces lividanscells.

The introduction of DNA into a Bacillus cell may be effected byprotoplast transformation (see, e.g., Chang and Cohen, 1979, Mol. Gen.Genet. 168: 111-115), competent cell transformation (see, e.g., Youngand Spizizen, 1961, J. Bacteriol. 81: 823-829, or Dubnau andDavidoff-Abelson, 1971, J. Mol. Biol. 56: 209-221), electroporation(see, e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), orconjugation (see, e.g., Koehler and Thorne, 1987, J. Bacteriol. 169:5271-5278). The introduction of DNA into an E. coli cell may be effectedby protoplast transformation (see, e.g., Hanahan, 1983, J. Mol. Biol.166: 557-580) or electroporation (see, e.g., Dower et al., 1988, NucleicAcids Res. 16: 6127-6145). The introduction of DNA into a Streptomycescell may be effected by protoplast transformation, electroporation (see,e.g., Gong et al., 2004, Folia Microbiol. (Praha) 49: 399-405),conjugation (see, e.g., Mazodier et al., 1989, J. Bacteriol. 171:3583-3585), or transduction (see, e.g., Burke et al., 2001, Proc. Natl.Acad. Sci. USA 98: 6289-6294). The introduction of DNA into aPseudomonas cell may be effected by electroporation (see, e.g., Choi etal., 2006, J. Microbiol. Methods 64: 391-397) or conjugation (see, e.g.,Pinedo and Smets, 2005, Appl. Environ. Microbiol. 71: 51-57). Theintroduction of DNA into a Streptococcus cell may be effected by naturalcompetence (see, e.g., Perry and Kuramitsu, 1981, Infect. Immun. 32:1295-1297), protoplast transformation (see, e.g., Catt and Jollick,1991, Microbios 68: 189-207), electroporation (see, e.g., Buckley etal., 1999, Appl. Environ. Microbiol. 65: 3800-3804), or conjugation(see, e.g., Clewell, 1981, Microbiol. Rev. 45: 409-436). However, anymethod known in the art for introducing DNA into a host cell can beused.

The host cell may also be a eukaryote, such as a mammalian, insect,plant, or fungal cell.

The host cell may be a fungal cell. “Fungi” as used herein includes thephyla Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota as wellas the Oomycota and all mitosporic fungi (as defined by Hawksworth etal., In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition,1995, CAB International, University Press, Cambridge, UK).

The fungal host cell may be a yeast cell. “Yeast” as used hereinincludes ascosporogenous yeast (Endomycetales), basidiosporogenousyeast, and yeast belonging to the Fungi Imperfecti (Blastomycetes).Since the classification of yeast may change in the future, for thepurposes of this invention, yeast shall be defined as described inBiology and Activities of Yeast (Skinner, Passmore, and Davenport,editors, Soc. App. Bacteriol. Symposium Series No. 9, 1980).

The yeast host cell may be a Candida, Hansenula, Kluyveromyces, Pichia,Saccharomyces, Schizosaccharomyces, or Yarrowia cell, such as aKluyveromyces lactis, Saccharomyces carlsbergensis, Saccharomycescerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii,Saccharomyces kluyveri, Saccharomyces norbensis, Saccharomycesoviformis, or Yarrowia lipolytica cell.

The fungal host cell may be a filamentous fungal cell. “Filamentousfungi” include all filamentous forms of the subdivision Eumycota andOomycota (as defined by Hawksworth et al., 1995, supra). The filamentousfungi are generally characterized by a mycelial wall composed of chitin,cellulose, glucan, chitosan, mannan, and other complex polysaccharides.Vegetative growth is by hyphal elongation and carbon catabolism isobligately aerobic. In contrast, vegetative growth by yeasts such asSaccharomyces cerevisiae is by budding of a unicellular thallus andcarbon catabolism may be fermentative.

The filamentous fungal host cell may be an Acremonium, Aspergillus,Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus,Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe,Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces,Penicillium, Phanerochaete, Phlebia, Piromyces, Pleurotus,Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium,Trametes, or Trichoderma cell.

For example, the filamentous fungal host cell may be an Aspergillusawamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillusjaponicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae,Bjerkandera adusta, Ceriporiopsis aneirina, Ceriporiopsis caregiea,Ceriporiopsis gilvescens, Ceriporiopsis pannocinta, Ceriporiopsisrivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora,Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporiumlucknowense, Chrysosporium merdarium, Chrysosporium pannicola,Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporiumzonatum, Coprinus cinereus, Coriolus hirsutus, Fusarium bactridioides,Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsuiphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Humicola insolens, Humicola lanuginosa, Mucor miehei,Myceliophthora thermophila, Neurospora crassa, Penicillium purpurogenum,Phanerochaete chrysosporium, Phiebia radiata, Pleurotus eryngii,Thielavia terrestris, Trametes villosa, Trametes versicolor, Trichodermaharzianum, Trichoderma koningii, Trichoderma longibrachiatum,Trichoderma reesei, or Trichoderma viride cell.

Fungal cells may be transformed by a process involving protoplastformation, transformation of the protoplasts, and regeneration of thecell wall in a manner known per se. Suitable procedures fortransformation of Aspergillus and Trichoderma host cells are describedin EP 238023, Yelton et al., 1984, Proc. Natl. Acad. Sci. USA 81:1470-1474, and Christensen et al., 1988, Bio/Technology 6: 1419-1422.Suitable methods for transforming Fusarium species are described byMalardier et al., 1989, Gene 78: 147-156, and WO 96/00787. Yeast may betransformed using the procedures described by Becker and Guarente, InAbelson, J. N. and Simon, M. I., editors, Guide to Yeast Genetics andMolecular Biology, Methods in Enzymology, Volume 194, pp 182-187,Academic Press, Inc., New York; Ito et al., 1983, J. Bacteriol. 153:163; and Hinnen et al., 1978, Proc. Natl. Acad. Sci. USA 75: 1920.

Methods of Production

The present invention also relates to methods of producing a polypeptideof the present invention, comprising (a) cultivating a cell, which inits wild-type form produces the polypeptide, under conditions conducivefor production of the polypeptide; and (b) recovering the polypeptide.

In one aspect, the cell is a Chaetomium cell. In another aspect, thecell is a Chaetomium senegalense cell. In another aspect, the cell is aChaetomium thermophilum cell.

In another aspect, the cell is a Corynascus cell. In another aspect, thecell is a Corynascus thermophilus cell.

In another aspect, the cell is a Malbranchea cell. In another aspect,the cell is a Malbranchea cinnamomea cell.

In another aspect, the cell is a Melanocarpus cell. In another aspect,the cell is a Melanocarpus albomyces cell.

In another aspect, the cell is a Remersonia cell. In another aspect, thecell is a Remersonia thermophila cell.

In another aspect, the cell is a Rhizomucor cell. In another aspect, thecell is a Rhizomucor miehei cell.

In another aspect, the cell is a Scytalidium cell. In another aspect,the cell is a Scytalidium indonesiacum cell.

In another aspect, the cell is a Talaromyces cell. In another aspect,the cell is a Talaromyces byssochlamydoides cell. In another aspect, thecell is a Talaromyces emersonii cell. In another aspect, the cell is aTalaromyces leycettanus cell. In another aspect, the cell is aTalaromyces thermophilus cell.

In another aspect, the cell is a Thermoascus cell. In another aspect,the cell is a Thermoascus aurantiacus cell.

In another aspect, the cell is a Thermomyces cell. In another aspect,the cell is a Thermomyces lanuginosus cell.

In another aspect, the cell is a Thermomucor cell. In another aspect,the cell is a Thermomucor indicae-seudaticae cell.

The present invention also relates to methods of producing a polypeptideof the present invention, comprising (a) cultivating a recombinant hostcell of the present invention under conditions conducive for productionof the polypeptide; and (b) recovering the polypeptide.

The cells are cultivated in a nutrient medium suitable for production ofthe polypeptide using methods known in the art. For example, the cellsmay be cultivated by shake flask cultivation, or small-scale orlarge-scale fermentation (including continuous, batch, fed-batch, orsolid state fermentations) in laboratory or industrial fermentors in asuitable medium and under conditions allowing the polypeptide to beexpressed and/or isolated. The cultivation takes place in a suitablenutrient medium comprising carbon and nitrogen sources and inorganicsalts, using procedures known in the art. Suitable media are availablefrom commercial suppliers or may be prepared according to publishedcompositions (e.g., in catalogues of the American Type CultureCollection). If the polypeptide is secreted into the nutrient medium,the polypeptide can be recovered directly from the medium. If thepolypeptide is not secreted, it can be recovered from cell lysates.

The polypeptide may be detected using methods known in the art that arespecific for the polypeptides. These detection methods include, but arenot limited to, use of specific antibodies, formation of an enzymeproduct, or disappearance of an enzyme substrate. For example, an enzymeassay may be used to determine the activity of the polypeptide.

The polypeptide may be recovered using methods known in the art. Forexample, the polypeptide may be recovered from the nutrient medium byconventional procedures including, but not limited to, collection,centrifugation, filtration, extraction, spray-drying, evaporation, orprecipitation. In one aspect, the whole fermentation broth is recovered.

The polypeptide may be purified by a variety of procedures known in theart including, but not limited to, chromatography (e.g., ion exchange,affinity, hydrophobic, chromatofocusing, and size exclusion),electrophoretic procedures (e.g., preparative isoelectric focusing),differential solubility (e.g., ammonium sulfate precipitation),SDS-PAGE, or extraction (see, e.g., Protein Purification, Janson andRyden, editors, VCH Publishers, New York, 1989) to obtain substantiallypure polypeptides.

In an alternative aspect, the polypeptide is not recovered, but rather ahost cell of the present invention expressing the polypeptide is used asa source of the polypeptide.

Plants

The present invention also relates to isolated plants, e.g., atransgenic plant, plant part, or plant cell, comprising a polynucleotideof the present invention so as to express and produce a polypeptide inrecoverable quantities. The polypeptide may be recovered from the plantor plant part. Alternatively, the plant or plant part containing thepolypeptide may be used as such for improving the quality of a food orfeed, e.g., improving nutritional value, palatability, and rheologicalproperties, or to destroy an antinutritive factor.

The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous(a monocot). Examples of monocot plants are grasses, such as meadowgrass (blue grass, Poa), forage grass such as Festuca, Lolium, temperategrass, such as Agrostis, and cereals, e.g., wheat, oats, rye, barley,rice, sorghum, and maize (corn).

Examples of dicot plants are tobacco, legumes, such as lupins, potato,sugar beet, pea, bean and soybean, and cruciferous plants (familyBrassicaceae), such as cauliflower, rape seed, and the closely relatedmodel organism Arabidopsis thaliana.

Examples of plant parts are stem, callus, leaves, root, fruits, seeds,and tubers as well as the individual tissues comprising these parts,e.g., epidermis, mesophyll, parenchyme, vascular tissues, meristems.Specific plant cell compartments, such as chloroplasts, apoplasts,mitochondria, vacuoles, peroxisomes and cytoplasm are also considered tobe a plant part. Furthermore, any plant cell, whatever the tissueorigin, is considered to be a plant part. Likewise, plant parts such asspecific tissues and cells isolated to facilitate the utilization of theinvention are also considered plant parts, e.g., embryos, endosperms,aleurone and seed coats.

Also included within the scope of the present invention are the progenyof such plants, plant parts, and plant cells.

The transgenic plant or plant cell expressing the polypeptide may beconstructed in accordance with methods known in the art. In short, theplant or plant cell is constructed by incorporating one or moreexpression constructs encoding the polypeptide into the plant hostgenome or chloroplast genome and propagating the resulting modifiedplant or plant cell into a transgenic plant or plant cell.

The expression construct is conveniently a nucleic acid construct thatcomprises a polynucleotide encoding a polypeptide operably linked withappropriate regulatory sequences required for expression of thepolynucleotide in the plant or plant part of choice. Furthermore, theexpression construct may comprise a selectable marker useful foridentifying plant cells into which the expression construct has beenintegrated and DNA sequences necessary for introduction of the constructinto the plant in question (the latter depends on the DNA introductionmethod to be used).

The choice of regulatory sequences, such as promoter and terminatorsequences and optionally signal or transit sequences, is determined, forexample, on the basis of when, where, and how the polypeptide is desiredto be expressed. For instance, the expression of the gene encoding apolypeptide may be constitutive or inducible, or may be developmental,stage or tissue specific, and the gene product may be targeted to aspecific tissue or plant part such as seeds or leaves. Regulatorysequences are, for example, described by Tague et al., 1988, PlantPhysiology 86: 506.

For constitutive expression, the 35S-CaMV, the maize ubiquitin 1, or therice actin 1 promoter may be used (Franck et al., 1980, Cell 21:285-294; Christensen et al., 1992, Plant Mol. Biol. 18: 675-689; Zhanget al., 1991, Plant Cell 3: 1155-1165). Organ-specific promoters may be,for example, a promoter from storage sink tissues such as seeds, potatotubers, and fruits (Edwards and Coruzzi, 1990, Ann. Rev. Genet. 24:275-303), or from metabolic sink tissues such as meristems (Ito et al.,1994, Plant Mol. Biol. 24: 863-878), a seed specific promoter such asthe glutelin, prolamin, globulin, or albumin promoter from rice (Wu etal., 1998, Plant Cell Physiol. 39: 885-889), a Vicia faba promoter fromthe legumin B4 and the unknown seed protein gene from Vicia faba (Conradet al., 1998, J. Plant Physiol. 152: 708-711), a promoter from a seedoil body protein (Chen et al., 1998, Plant Cell Physiol. 39: 935-941),the storage protein napA promoter from Brassica napus, or any other seedspecific promoter known in the art, e.g., as described in WO 91/14772.Furthermore, the promoter may be a leaf specific promoter such as therbcs promoter from rice or tomato (Kyozuka et al., 1993, Plant Physiol.102: 991-1000), the chlorella virus adenine methyltransferase genepromoter (Mitra and Higgins, 1994, Plant Mol. Biol. 26: 85-93), the aldPgene promoter from rice (Kagaya et al., 1995, Mol. Gen. Genet. 248:668-674), or a wound inducible promoter such as the potato pin2 promoter(Xu et al., 1993, Plant Mol. Biol. 22: 573-588). Likewise, the promotermay be induced by abiotic treatments such as temperature, drought, oralterations in salinity or induced by exogenously applied substancesthat activate the promoter, e.g., ethanol, oestrogens, plant hormonessuch as ethylene, abscisic acid, and gibberellic acid, and heavy metals.

A promoter enhancer element may also be used to achieve higherexpression of a polypeptide in the plant. For instance, the promoterenhancer element may be an intron that is placed between the promoterand the polynucleotide encoding a polypeptide. For instance, Xu et al.,1993, supra, disclose the use of the first intron of the rice actin 1gene to enhance expression.

The selectable marker gene and any other parts of the expressionconstruct may be chosen from those available in the art.

The nucleic acid construct is incorporated into the plant genomeaccording to conventional techniques known in the art, includingAgrobacterium-mediated transformation, virus-mediated transformation,microinjection, particle bombardment, biolistic transformation, andelectroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990,Bio/Technology 8: 535; Shimamoto et al., 1989, Nature 338: 274).

Agrobacterium tumefaciens-mediated gene transfer is a method forgenerating transgenic dicots (for a review, see Hooykas andSchilperoort, 1992, Plant Mol. Biol. 19: 15-38) and for transformingmonocots, although other transformation methods may be used for theseplants. A method for generating transgenic monocots is particlebombardment (microscopic gold or tungsten particles coated with thetransforming DNA) of embryonic calli or developing embryos (Christou,1992, Plant J. 2: 275-281; Shimamoto, 1994, Curr. Opin. Biotechnol. 5:158-162; Vasil et al., 1992, Bio/Technology 10: 667-674). An alternativemethod for transformation of monocots is based on protoplasttransformation as described by Omirulleh et al., 1993, Plant Mol. Biol.21: 415-428. Additional transformation methods include those describedin U.S. Pat. Nos. 6,395,966 and 7,151,204 (both of which are hereinincorporated by reference in their entirety).

Following transformation, the transformants having incorporated theexpression construct are selected and regenerated into whole plantsaccording to methods well known in the art. Often the transformationprocedure is designed for the selective elimination of selection geneseither during regeneration or in the following generations by using, forexample, co-transformation with two separate T-DNA constructs or sitespecific excision of the selection gene by a specific recombinase.

In addition to direct transformation of a particular plant genotype witha construct of the present invention, transgenic plants may be made bycrossing a plant having the construct to a second plant lacking theconstruct. For example, a construct encoding a polypeptide can beintroduced into a particular plant variety by crossing, without the needfor ever directly transforming a plant of that given variety. Therefore,the present invention encompasses not only a plant directly regeneratedfrom cells which have been transformed in accordance with the presentinvention, but also the progeny of such plants. As used herein, progenymay refer to the offspring of any generation of a parent plant preparedin accordance with the present invention. Such progeny may include a DNAconstruct prepared in accordance with the present invention. Crossingresults in the introduction of a transgene into a plant line by crosspollinating a starting line with a donor plant line. Non-limitingexamples of such steps are described in U.S. Pat. No. 7,151,204.

Plants may be generated through a process of backcross conversion. Forexample, plants include plants referred to as a backcross convertedgenotype, line, inbred, or hybrid.

Genetic markers may be used to assist in the introgression of one ormore transgenes of the invention from one genetic background intoanother. Marker assisted selection offers advantages relative toconventional breeding in that it can be used to avoid errors caused byphenotypic variations. Further, genetic markers may provide dataregarding the relative degree of elite germplasm in the individualprogeny of a particular cross. For example, when a plant with a desiredtrait which otherwise has a non-agronomically desirable geneticbackground is crossed to an elite parent, genetic markers may be used toselect progeny which not only possess the trait of interest, but alsohave a relatively large proportion of the desired germplasm. In thisway, the number of generations required to introgress one or more traitsinto a particular genetic background is minimized.

The present invention also relates to methods of producing a polypeptideof the present invention comprising (a) cultivating a transgenic plantor a plant cell comprising a polynucleotide encoding the polypeptideunder conditions conducive for production of the polypeptide; and (b)recovering the polypeptide.

Removal or Reduction of Cellulolytic or Hemicellulolytic Activity

The present invention also relates to methods of producing a mutant of aparent cell, which comprises disrupting or deleting a polynucleotide, ora portion thereof, encoding a polypeptide of the present invention,which results in the mutant cell producing less of the polypeptide thanthe parent cell when cultivated under the same conditions.

The mutant cell may be constructed by reducing or eliminating expressionof the polynucleotide using methods well known in the art, for example,insertions, disruptions, replacements, or deletions. In a preferredaspect, the polynucleotide is inactivated. The polynucleotide to bemodified or inactivated may be, for example, the coding region or a partthereof essential for activity, or a regulatory element required forexpression of the coding region. An example of such a regulatory orcontrol sequence may be a promoter sequence or a functional partthereof, i.e., a part that is sufficient for affecting expression of thepolynucleotide. Other control sequences for possible modificationinclude, but are not limited to, a leader, polyadenylation sequence,propeptide sequence, signal peptide sequence, transcription terminator,and transcriptional activator.

Modification or inactivation of the polynucleotide may be performed bysubjecting the parent cell to mutagenesis and selecting for mutant cellsin which expression of the polynucleotide has been reduced oreliminated. The mutagenesis, which may be specific or random, may beperformed, for example, by use of a suitable physical or chemicalmutagenizing agent, by use of a suitable oligonucleotide, or bysubjecting the DNA sequence to PCR generated mutagenesis. Furthermore,the mutagenesis may be performed by use of any combination of thesemutagenizing agents.

Examples of a physical or chemical mutagenizing agent suitable for thepresent purpose include ultraviolet (UV) irradiation, hydroxylamine,N-methyl-N′-nitro-N-nitrosoguanidine (MNNG), O-methyl hydroxylamine,nitrous acid, ethyl methane sulphonate (EMS), sodium bisulphite, formicacid, and nucleotide analogues.

When such agents are used, the mutagenesis is typically performed byincubating the parent cell to be mutagenized in the presence of themutagenizing agent of choice under suitable conditions, and screeningand/or selecting for mutant cells exhibiting reduced or no expression ofthe gene.

Modification or inactivation of the polynucleotide may be accomplishedby insertion, substitution, or deletion of one or more nucleotides inthe gene or a regulatory element required for transcription ortranslation thereof. For example, nucleotides may be inserted or removedso as to result in the introduction of a stop codon, the removal of thestart codon, or a change in the open reading frame. Such modification orinactivation may be accomplished by site-directed mutagenesis or PCRgenerated mutagenesis in accordance with methods known in the art.Although, in principle, the modification may be performed in vivo, i.e.,directly on the cell expressing the polynucleotide to be modified, it ispreferred that the modification be performed in vitro as exemplifiedbelow.

An example of a convenient way to eliminate or reduce expression of apolynucleotide is based on techniques of gene replacement, genedeletion, or gene disruption. For example, in the gene disruptionmethod, a nucleic acid sequence corresponding to the endogenouspolynucleotide is mutagenized in vitro to produce a defective nucleicacid sequence that is then transformed into the parent cell to produce adefective gene. By homologous recombination, the defective nucleic acidsequence replaces the endogenous polynucleotide. It may be desirablethat the defective polynucleotide also encodes a marker that may be usedfor selection of transformants in which the polynucleotide has beenmodified or destroyed. In an aspect, the polynucleotide is disruptedwith a selectable marker such as those described herein.

The present invention also relates to methods of inhibiting theexpression of a polypeptide having cellobiohydrolase, endoglucanase,cellulolytic enhancing, or xylanase activity in a cell, comprisingadministering to the cell or expressing in the cell a double-strandedRNA (dsRNA) molecule, wherein the dsRNA comprises a subsequence of apolynucleotide of the present invention. In a preferred aspect, thedsRNA is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplexnucleotides in length.

The dsRNA is preferably a small interfering RNA (siRNA) or a micro RNA(miRNA). In a preferred aspect, the dsRNA is small interfering RNA forinhibiting transcription. In another preferred aspect, the dsRNA ismicro RNA for inhibiting translation.

The present invention also relates to such double-stranded RNA (dsRNA)molecules, comprising a portion of the polypeptide coding sequence ofSEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9,SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO:19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ IDNO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47,SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO:57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ IDNO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, orSEQ ID NO: 77 for inhibiting expression of the polypeptide in a cell.While the present invention is not limited by any particular mechanismof action, the dsRNA can enter a cell and cause the degradation of asingle-stranded RNA (ssRNA) of similar or identical sequences, includingendogenous mRNAs. When a cell is exposed to dsRNA, mRNA from thehomologous gene is selectively degraded by a process called RNAinterference (RNAi).

The dsRNAs of the present invention can be used in gene-silencing. Inone aspect, the invention provides methods to selectively degrade RNAusing a dsRNAi of the present invention. The process may be practiced invitro, ex vivo or in vivo. In one aspect, the dsRNA molecules can beused to generate a loss-of-function mutation in a cell, an organ or ananimal. Methods for making and using dsRNA molecules to selectivelydegrade RNA are well known in the art; see, for example, U.S. Pat. Nos.6,489,127; 6,506,559; 6,511,824; and 6,515,109.

The present invention further relates to a mutant cell of a parent cellthat comprises a disruption or deletion of a polynucleotide encoding thepolypeptide or a control sequence thereof or a silenced gene encodingthe polypeptide, which results in the mutant cell producing less of thepolypeptide or no polypeptide compared to the parent cell.

The polypeptide-deficient mutant cells are particularly useful as hostcells for expression of native and heterologous polypeptides. Therefore,the present invention further relates to methods of producing a nativeor heterologous polypeptide, comprising (a) cultivating the mutant cellunder conditions conducive for production of the polypeptide; and (b)recovering the polypeptide. The term “heterologous polypeptides” meanspolypeptides that are not native to the host cell, e.g., a variant of anative protein. The host cell may comprise more than one copy of apolynucleotide encoding the native or heterologous polypeptide.

The methods used for cultivation and purification of the product ofinterest may be performed by methods known in the art.

The methods of the present invention for producing an essentiallycellobiohydrolase, endoglucanase, cellulolytic enhancing, orxylanase-free product is of particular interest in the production ofeukaryotic polypeptides, in particular fungal proteins such as enzymes.The cellobiohydrolase, endoglucanase, cellulolytic enhancing, orxylanase-deficient cells may also be used to express heterologousproteins of pharmaceutical interest such as hormones, growth factors,receptors, and the like. The term “eukaryotic polypeptides” includes notonly native polypeptides, but also those polypeptides, e.g., enzymes,which have been modified by amino acid substitutions, deletions oradditions, or other such modifications to enhance activity,thermostability, pH tolerance and the like.

In a further aspect, the present invention relates to a protein productessentially free from cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity that is produced by a method of thepresent invention.

Compositions

The present invention also relates to compositions comprising apolypeptide of the present invention. Preferably, the compositions areenriched in such a polypeptide. The term “enriched” indicates that thecellobiohydrolase, endoglucanase, cellulolytic enhancing, or xylanaseactivity of the composition has been increased, e.g., with an enrichmentfactor of at least 1.1.

The compositions may comprise a polypeptide of the present invention asthe major enzymatic component, e.g., a mono-component composition.Alternatively, the compositions may comprise multiple enzymaticactivities, such as one or more (e.g., several) additional enzymesselected from the group consisting of a cellulase, a polypeptide havingcellulolytic enhancing activity, a hemicellulase, an esterase, anexpansin, a laccase, a ligninolytic enzyme, a pectinase, a peroxidase, aprotease, and a swollenin.

The compositions may be prepared in accordance with methods known in theart and may be in the form of a liquid or a dry composition. Thecompositions may be stabilized in accordance with methods known in theart.

In one embodiment, the composition further comprises one or more enzymesselected from the group consisting of one or more (e.g., several)xylanases, mannanases, glucanases, cellulases, lipases, esterases,proteases, endoglycosidases, endo-beta-1,4-glucanases, beta-glucanases,endo-beta-1,3(4)-glucanases, cutinases, peroxidases, catalases,laccases, amylases, glucoamylases, pectinases, reductases, oxidases,phenoloxidases, ligninases, pullulanases, arabinanases, hemicellulases,mannanases, xyloglucanases, xylanases, mannanases, glucanases, pectinacetyl esterases, rhamnogalacturonan acetyl esterases,polygalacturonases, rhamnogalacturonases, galactanases, pectin lyases,pectin methylesterases, and transglutaminases.

The compositions may be prepared in accordance with methods known in theart and may have any physical appearance such as liquid, paste or solid.For instance, the polypeptide composition may be formulated usingmethods known to the art of formulating enzymes and/or pharmaceuticalproducts, e.g., into coated or uncoated granules or micro granules. Thepolypeptide to be included in the composition may be stabilized inaccordance with methods known in the art, e.g., by stabilizing thepolypeptide in the composition by adding an antioxidant or reducingagent to limit oxidation or the polypeptide may be stabilized by addingpolymers such as PVP, PVA, PEG or other suitable polymers known to bebeneficial to the stability of polypeptides in solid or liquidcompositions.

The compositions may be a fermentation broth formulation or a cellcomposition, as described herein. Consequently, the present inventionalso relates to fermentation broth formulations and cell compositionscomprising a polypeptide having cellobiohydrolase, endoglucanase,cellulolytic enhancing, or xylanase activity of the present invention.In some embodiments, the composition is a cell-killed whole brothcontaining organic acid(s), killed cells and/or cell debris, and culturemedium.

The term “fermentation broth” as used herein refers to a preparationproduced by cellular fermentation that undergoes no or minimal recoveryand/or purification. For example, fermentation broths are produced whenmicrobial cultures are grown to saturation, incubated undercarbon-limiting conditions to allow protein synthesis (e.g., expressionof enzymes by host cells) and secretion into cell culture medium. Thefermentation broth can contain unfractionated or fractionated contentsof the fermentation materials derived at the end of the fermentation.Typically, the fermentation broth is unfractionated and comprises thespent culture medium and cell debris present after the microbial cells(e.g., filamentous fungal cells) are removed, e.g., by centrifugation.In some embodiments, the fermentation broth contains spent cell culturemedium, extracellular enzymes, and viable and/or nonviable microbialcells.

In an embodiment, the fermentation broth formulation and cellcompositions comprise a first organic acid component comprising at leastone 1-5 carbon organic acid and/or a salt thereof and a second organicacid component comprising at least one 6 or more carbon organic acidand/or a salt thereof. In a specific embodiment, the first organic acidcomponent is acetic acid, formic acid, propionic acid, a salt thereof,or a mixture of two or more of the foregoing and the second organic acidcomponent is benzoic acid, cyclohexanecarboxylic acid, 4-methylvalericacid, phenylacetic acid, a salt thereof, or a mixture of two or more ofthe foregoing.

In one aspect, the composition contains an organic acid(s), andoptionally further contains killed cells and/or cell debris. In oneembodiment, the killed cells and/or cell debris are removed from acell-killed whole broth to provide a composition that is free of thesecomponents.

The fermentation broth formulations or cell compostions may furthercomprise a preservative and/or anti-microbial (e.g., bacteriostatic)agent, including, but not limited to, sorbitol, sodium chloride,potassium sorbate, and others known in the art.

The cell-killed whole broth or composition may further comprise one ormore enzyme activities such as acetylxylan esterase,alpha-arabinofuranosidase, alpha-galactosidase, alpha-glucuronidase,amylase, arabinanase, arabinofuranosidase, beta-galactosidase,beta-glucosidase, cellobiohydrolase, endoglucanase,endo-beta-1,3(4)-glucanase, ferrulic acid esterase, galactanase,glucoamylase, glucohydrolase, hybrid peroxidases, with combinedproperties of lignin peroxidases and manganese-dependent peroxidases,laccase, lignin peroxidase, manganese-dependent peroxidases, mannanase,mannan acetyl esterase, mannosidase, pectate lyase, pectin acetylesterase, pectinase lyase, pectin methyl esterase, polygalacturonase,protease, rhamnogalacturonan lyase, rhamnogalacturonan acetyl esterase,rhamnogalacturonase, xylanase, xylogalacturonosidase, xylogalacturonase,xyloglucanase, and xylosidase.

In some embodiments, the cell-killed whole broth or composition includescellulolytic enzymes including, but not limited to, (i) endoglucanases(EG) or 1,4-D-glucan-4-glucanohydrolases (EC 3.2.1.4), (ii)exoglucanases, including 1,4-D-glucan glucanohydrolases (also known ascellodextnnases) (EC 3.2.1.74) and 1,4-D-glucan cellobiohydrolases(exo-cellobiohydrolases, CBH) (EC 3.2.1.91), and (iii) beta-glucosidase(BG) or beta-glucoside glucohydrolases (EC 3.2.1.21).

The cell-killed whole broth or composition may contain theunfractionated contents of the fermentation materials derived at the endof the fermentation. Typically, the cell-killed whole broth orcomposition contains the spent culture medium and cell debris presentafter the microbial cells (e.g., filamentous fungal cells) are grown tosaturation, incubated under carbon-limiting conditions to allow proteinsynthesis (e.g., expression of cellulase and/or glucosidase enzyme(s)).In some embodiments, the cell-killed whole broth or composition containsthe spent cell culture medium, extracellular enzymes, and killedfilamentous fungal cells. In some embodiments, the microbial cellspresent in the cell-killed whole broth or composition can bepermeabilized and/or lysed using methods known in the art.

A whole broth or cell composition as described herein is typically aliquid, but may contain insoluble components, such as killed cells, celldebris, culture media components, and/or insoluble enzyme(s). In someembodiments, insoluble components may be removed to provide a clarifiedliquid composition.

The whole broth formulations and cell compositions of the presentinvention may be produced by a method described in WO 90/15861 or WO2010/096673.

Examples are given below of preferred uses of the compositions of thepresent invention. The dosage of the composition and other conditionsunder which the composition is used may be determined on the basis ofmethods known in the art.

Uses

The present invention is also directed to the following processes forusing the polypeptides having cellobiohydrolase, endoglucanase,cellulolytic enhancing, or xylanase activity, or compositions thereof.

The present invention also relates to processes for degrading orconverting a cellulosic or xylan-containing material, comprising:treating the cellulosic or xylan-containing material with an enzymecomposition in the presence of a polypeptide having cellobiohydrolase,endoglucanase, cellulolytic enhancing, or xylanase activity of thepresent invention. In one aspect, the processes further compriserecovering the degraded or converted cellulosic or xylan-containingmaterial. Soluble products of degradation or conversion of thecellulosic or xylan-containing material can be separated from insolublecellulosic or xylan-containing material using a method known in the artsuch as, for example, centrifugation, filtration, or gravity settling.

The present invention also relates to processes of producing afermentation product, comprising: (a) saccharifying a cellulosic orxylan-containing material with an enzyme composition in the presence ofa polypeptide having cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity of the present invention; (b) fermentingthe saccharified cellulosic or xylan-containing material with one ormore (e.g., several) fermenting microorganisms to produce thefermentation product; and (c) recovering the fermentation product fromthe fermentation.

The present invention also relates to processes of fermenting acellulosic or xylan-containing material, comprising: fermenting thecellulosic or xylan-containing material with one or more (e.g., several)fermenting microorganisms, wherein the cellulosic or xylan-containingmaterial is saccharified with an enzyme composition in the presence of apolypeptide having cellobiohydrolase, endoglucanase, cellulolyticenhancing, or xylanase activity of the present invention. In one aspect,the fermenting of the cellulosic or xylan-containing material produces afermentation product. In another aspect, the processes further compriserecovering the fermentation product from the fermentation.

The present invention also relates to use of a cellulose-degradingpolypeptide of the present invention in a detergent composition, intextile finishing processes, purification of polypeptides, forimmobilization of active enzymes, for baking, for manufacturing ofbiofuel, for modification of plant cell walls, or for processing ofcellulose fibre.

The processes of the present invention can be used to saccharify thecellulosic or xylan-containing material to fermentable sugars and toconvert the fermentable sugars to many useful fermentation products,e.g., fuel, potable ethanol, and/or platform chemicals (e.g., acids,alcohols, ketones, gases, and the like). The production of a desiredfermentation product from the cellulosic or xylan-containing materialtypically involves pretreatment, enzymatic hydrolysis(saccharification), and fermentation.

The processing of the cellulosic or xylan-containing material accordingto the present invention can be accomplished using methods conventionalin the art. Moreover, the processes of the present invention can beimplemented using any conventional biomass processing apparatusconfigured to operate in accordance with the invention.

Hydrolysis (saccharification) and fermentation, separate orsimultaneous, include, but are not limited to, separate hydrolysis andfermentation (SHF); simultaneous saccharification and fermentation(SSF); simultaneous saccharification and co-fermentation (SSCF); hybridhydrolysis and fermentation (HHF); separate hydrolysis andco-fermentation (SHCF); hybrid hydrolysis and co-fermentation (HHCF);and direct microbial conversion (DMC), also sometimes calledconsolidated bioprocessing (CBP). SHF uses separate process steps tofirst enzymatically hydrolyze the cellulosic material to fermentablesugars, e.g., glucose, cellobiose, and pentose monomers, and thenferment the fermentable sugars to ethanol. In SSF, the enzymatichydrolysis of the cellulosic material and the fermentation of sugars toethanol are combined in one step (Philippidis, G. P., 1996, Cellulosebioconversion technology, in Handbook on Bioethanol: Production andUtilization, Wyman, C. E., ed., Taylor & Francis, Washington, D.C.,179-212). SSCF involves the co-fermentation of multiple sugars (Sheehan,J., and Himmel, M., 1999, Enzymes, energy and the environment: Astrategic perspective on the U.S. Department of Energy's research anddevelopment activities for bioethanol, Biotechnol. Prog. 15: 817-827).HHF involves a separate hydrolysis step, and in addition a simultaneoussaccharification and hydrolysis step, which can be carried out in thesame reactor. The steps in an HHF process can be carried out atdifferent temperatures, i.e., high temperature enzymaticsaccharification followed by SSF at a lower temperature that thefermentation strain can tolerate. DMC combines all three processes(enzyme production, hydrolysis, and fermentation) in one or more (e.g.,several) steps where the same organism is used to produce the enzymesfor conversion of the cellulosic material to fermentable sugars and toconvert the fermentable sugars into a final product (Lynd, L. R.,Weimer, P. J., van Zyl, W. H., and Pretorius, I. S., 2002, Microbialcellulose utilization: Fundamentals and biotechnology, Microbiol. Mol.Biol. Reviews 66: 506-577). It is understood herein that any methodknown in the art comprising pretreatment, enzymatic hydrolysis(saccharification), fermentation, or a combination thereof, can be usedin the practicing the processes of the present invention.

A conventional apparatus can include a fed-batch stirred reactor, abatch stirred reactor, a continuous flow stirred reactor withultrafiltration, and/or a continuous plug-flow column reactor (Fernandade Castilhos Corazza, Flavio Faria de Moraes, Gisella Maria Zanin andIvo Neitzel, 2003, Optimal control in fed-batch reactor for thecellobiose hydrolysis, Acta Scientiarum. Technology 25: 33-38; Gusakov,A. V., and Sinitsyn, A. P., 1985, Kinetics of the enzymatic hydrolysisof cellulose: 1. A mathematical model for a batch reactor process, Enz.Microb. Technol. 7: 346-352), an attrition reactor (Ryu, S. K., and Lee,J. M., 1983, Bioconversion of waste cellulose by using an attritionbioreactor, Biotechnol. Bioeng. 25: 53-65), or a reactor with intensivestirring induced by an electromagnetic field (Gusakov, A. V., Sinitsyn,A. P., Davydkin, I. Y., Davydkin, V. Y., Protas, 0. V., 1996,Enhancement of enzymatic cellulose hydrolysis using a novel type ofbioreactor with intensive stirring induced by electromagnetic field,Appl. Biochem. Biotechnol. 56: 141-153). Additional reactor typesinclude fluidized bed, upflow blanket, immobilized, and extruder typereactors for hydrolysis and/or fermentation.

Pretreatment.

In practicing the processes of the present invention, any pretreatmentprocess known in the art can be used to disrupt plant cell wallcomponents of the cellulosic or xylan-containing material (Chandra etal., 2007, Substrate pretreatment: The key to effective enzymatichydrolysis of lignocellulosics?, Adv. Biochem. Engin./Biotechnol. 108:67-93; Galbe and Zacchi, 2007, Pretreatment of lignocellulosic materialsfor efficient bioethanol production, Adv. Biochem. Engin./Biotechnol.108: 41-65; Hendriks and Zeeman, 2009, Pretreatments to enhance thedigestibility of lignocellulosic biomass, Bioresource Technol. 100:10-18; Mosier et al., 2005, Features of promising technologies forpretreatment of lignocellulosic biomass, Bioresource Technol. 96:673-686; Taherzadeh and Karimi, 2008, Pretreatment of lignocellulosicwastes to improve ethanol and biogas production: A review, Int. J. ofMol. Sci. 9: 1621-1651; Yang and Wyman, 2008, Pretreatment: the key tounlocking low-cost cellulosic ethanol, Biofuels Bioproducts andBiorefining-Biofpr. 2: 26-40).

The cellulosic or xylan-containing material can also be subjected toparticle size reduction, sieving, pre-soaking, wetting, washing, and/orconditioning prior to pretreatment using methods known in the art.

Conventional pretreatments include, but are not limited to, steampretreatment (with or without explosion), dilute acid pretreatment, hotwater pretreatment, alkaline pretreatment, lime pretreatment, wetoxidation, wet explosion, ammonia fiber explosion, organosolvpretreatment, and biological pretreatment. Additional pretreatmentsinclude ammonia percolation, ultrasound, electroporation, microwave,supercritical CO₂, supercritical H₂O, ozone, ionic liquid, and gammairradiation pretreatments.

The cellulosic or xylan-containing material can be pretreated beforehydrolysis and/or fermentation. Pretreatment is preferably performedprior to the hydrolysis. Alternatively, the pretreatment can be carriedout simultaneously with enzyme hydrolysis to release fermentable sugars,such as glucose, xylose, and/or cellobiose. In most cases thepretreatment step itself results in some conversion of biomass tofermentable sugars (even in absence of enzymes).

Steam Pretreatment. In steam pretreatment, the cellulosic orxylan-containing material is heated to disrupt the plant cell wallcomponents, including lignin, hemicellulose, and cellulose to make thecellulose and other fractions, e.g., hemicellulose, accessible toenzymes. The cellulosic or xylan-containing material is passed to orthrough a reaction vessel where steam is injected to increase thetemperature to the required temperature and pressure and is retainedtherein for the desired reaction time. Steam pretreatment is preferablyperformed at 140-250° C., e.g., 160-200° C. or 170-190° C., where theoptimal temperature range depends on addition of a chemical catalyst.Residence time for the steam pretreatment is preferably 1-60 minutes,e.g., 1-30 minutes, 1-20 minutes, 3-12 minutes, or 4-10 minutes, wherethe optimal residence time depends on temperature range and addition ofa chemical catalyst. Steam pretreatment allows for relatively highsolids loadings, so that the cellulosic or xylan-containing material isgenerally only moist during the pretreatment. The steam pretreatment isoften combined with an explosive discharge of the material after thepretreatment, which is known as steam explosion, that is, rapid flashingto atmospheric pressure and turbulent flow of the material to increasethe accessible surface area by fragmentation (Duff and Murray, 1996,Bioresource Technology 855: 1-33; Galbe and Zacchi, 2002, Appl.Microbiol. Biotechnol. 59: 618-628; U.S. Patent Application No.20020164730). During steam pretreatment, hemicellulose acetyl groups arecleaved and the resulting acid autocatalyzes partial hydrolysis of thehemicellulose to monosaccharides and oligosaccharides. Lignin is removedto only a limited extent.

Chemical Pretreatment: The term “chemical treatment” refers to anychemical pretreatment that promotes the separation and/or release ofcellulose, hemicellulose, and/or lignin. Such a pretreatment can convertcrystalline cellulose to amorphous cellulose. Examples of suitablechemical pretreatment processes include, for example, dilute acidpretreatment, lime pretreatment, wet oxidation, ammonia fiber/freezeexplosion (AFEX), ammonia percolation (APR), ionic liquid, andorganosolv pretreatments.

A catalyst such as H₂SO₄ or SO₂ (typically 0.3 to 5% w/w) is often addedprior to steam pretreatment, which decreases the time and temperature,increases the recovery, and improves enzymatic hydrolysis (Ballesteroset al., 2006, Appl. Biochem. Biotechnol. 129-132: 496-508; Varga et al.,2004, Appl. Biochem. Biotechnol. 113-116: 509-523; Sassner et al., 2006,Enzyme Microb. Technol. 39: 756-762). In dilute acid pretreatment, thecellulosic or xylan-containing material is mixed with dilute acid,typically H₂SO₄, and water to form a slurry, heated by steam to thedesired temperature, and after a residence time flashed to atmosphericpressure. The dilute acid pretreatment can be performed with a number ofreactor designs, e.g., plug-flow reactors, counter-current reactors, orcontinuous counter-current shrinking bed reactors (Duff and Murray,1996, supra; Schell et al., 2004, Bioresource Technol. 91: 179-188; Leeet al., 1999, Adv. Biochem. Eng. Biotechnol. 65: 93-115).

Several methods of pretreatment under alkaline conditions can also beused. These alkaline pretreatments include, but are not limited to,sodium hydroxide, lime, wet oxidation, ammonia percolation (APR), andammonia fiber/freeze explosion (AFEX).

Lime pretreatment is performed with calcium oxide or calcium hydroxideat temperatures of 85-150° C. and residence times from 1 hour to severaldays (Wyman et al., 2005, Bioresource Technol. 96: 1959-1966; Mosier etal., 2005, Bioresource Technol. 96: 673-686). WO 2006/110891, WO2006/110899, WO 2006/110900, and WO 2006/110901 disclose pretreatmentmethods using ammonia.

Wet oxidation is a thermal pretreatment performed typically at 180-200°C. for 5-15 minutes with addition of an oxidative agent such as hydrogenperoxide or over-pressure of oxygen (Schmidt and Thomsen, 1998,Bioresource Technol. 64: 139-151; Palonen et al., 2004, Appl. Biochem.Biotechnol. 117: 1-17; Varga et al., 2004, Biotechnol. Bioeng. 88:567-574; Martin et al., 2006, J. Chem. Technol. Biotechnol. 81:1669-1677). The pretreatment is performed preferably at 1-40% drymatter, e.g., 2-30% dry matter or 5-20% dry matter, and often theinitial pH is increased by the addition of alkali such as sodiumcarbonate.

A modification of the wet oxidation pretreatment method, known as wetexplosion (combination of wet oxidation and steam explosion) can handledry matter up to 30%. In wet explosion, the oxidizing agent isintroduced during pretreatment after a certain residence time. Thepretreatment is then ended by flashing to atmospheric pressure (WO2006/032282).

Ammonia fiber explosion (AFEX) involves treating the cellulosic orxylan-containing material with liquid or gaseous ammonia at moderatetemperatures such as 90-150° C. and high pressure such as 17-20 bar for5-10 minutes, where the dry matter content can be as high as 60%(Gollapalli et al., 2002, Appl. Biochem. Biotechnol. 98: 23-35;Chundawat et al., 2007, Biotechnol. Bioeng. 96: 219-231; Alizadeh etal., 2005, Appl. Biochem. Biotechnol. 121: 1133-1141; Teymouri et al.,2005, Bioresource Technol. 96: 2014-2018). During AFEX pretreatmentcellulose and hemicelluloses remain relatively intact.Lignin-carbohydrate complexes are cleaved.

Organosolv pretreatment delignifies the cellulosic or xylan-containingmaterial by extraction using aqueous ethanol (40-60% ethanol) at160-200° C. for 30-60 minutes (Pan et al., 2005, Biotechnol. Bioeng. 90:473-481; Pan et al., 2006, Biotechnol. Bioeng. 94: 851-861; Kurabi etal., 2005, Appl. Biochem. Biotechnol. 121: 219-230). Sulphuric acid isusually added as a catalyst. In organosolv pretreatment, the majority ofhemicellulose and lignin is removed.

Other examples of suitable pretreatment methods are described by Schellet al., 2003, Appl. Biochem. and Biotechnol. Vol. 105-108, p. 69-85, andMosier et al., 2005, Bioresource Technology 96: 673-686, and U.S.Published Application 2002/0164730.

In one aspect, the chemical pretreatment is preferably carried out as adilute acid treatment, and more preferably as a continuous dilute acidtreatment. The acid is typically sulfuric acid, but other acids can alsobe used, such as acetic acid, citric acid, nitric acid, phosphoric acid,tartaric acid, succinic acid, hydrogen chloride, or mixtures thereof.Mild acid treatment is conducted in the pH range of preferably 1-5,e.g., 1-4 or 1-2.5. In one aspect, the acid concentration is in therange from preferably 0.01 to 10 wt % acid, e.g., 0.05 to 5 wt % acid or0.1 to 2 wt % acid. The acid is contacted with the cellulosic orxylan-containing material and held at a temperature in the range ofpreferably 140-200° C., e.g., 165-190° C., for periods ranging from 1 to60 minutes.

In another aspect, pretreatment takes place in an aqueous slurry. Inpreferred aspects, the cellulosic or xylan-containing material ispresent during pretreatment in amounts preferably between 10-80 wt %,e.g., 20-70 wt % or 30-60 wt %, such as around 40 wt %. The pretreatedcellulosic or xylan-containing material can be unwashed or washed usingany method known in the art, e.g., washed with water.

Mechanical Pretreatment or Physical Pretreatment: The term “mechanicalpretreatment” or “physical pretreatment” refers to any pretreatment thatpromotes size reduction of particles. For example, such pretreatment caninvolve various types of grinding or milling (e.g., dry milling, wetmilling, or vibratory ball milling).

The cellulosic or xylan-containing material can be pretreated bothphysically (mechanically) and chemically. Mechanical or physicalpretreatment can be coupled with steaming/steam explosion,hydrothermolysis, dilute or mild acid treatment, high temperature, highpressure treatment, irradiation (e.g., microwave irradiation), orcombinations thereof. In one aspect, high pressure means pressure in therange of preferably about 100 to about 400 psi, e.g., about 150 to about250 psi. In another aspect, high temperature means temperatures in therange of about 100 to about 300° C., e.g., about 140 to about 200° C. Ina preferred aspect, mechanical or physical pretreatment is performed ina batch-process using a steam gun hydrolyzer system that uses highpressure and high temperature as defined above, e.g., a Sunds Hydrolyzeravailable from Sunds Defibrator AB, Sweden. The physical and chemicalpretreatments can be carried out sequentially or simultaneously, asdesired.

Accordingly, in a preferred aspect, the cellulosic or xylan-containingmaterial is subjected to physical (mechanical) or chemical pretreatment,or any combination thereof, to promote the separation and/or release ofcellulose, hemicellulose, and/or lignin.

Biological Pretreatment: The term “biological pretreatment” refers toany biological pretreatment that promotes the separation and/or releaseof cellulose, hemicellulose, and/or lignin from the cellulosic orxylan-containing material. Biological pretreatment techniques caninvolve applying lignin-solubilizing microorganisms and/or enzymes (see,for example, Hsu, T.-A., 1996, Pretreatment of biomass, in Handbook onBioethanol: Production and Utilization, Wyman, C. E., ed., Taylor &Francis, Washington, D.C., 179-212; Ghosh and Singh, 1993,Physicochemical and biological treatments for enzymatic/microbialconversion of cellulosic biomass, Adv. Appl. Microbiol. 39: 295-333;McMillan, J. D., 1994, Pretreating lignocellulosic biomass: a review, inEnzymatic Conversion of Biomass for Fuels Production, Himmel, M. E.,Baker, J. O., and Overend, R. P., eds., ACS Symposium Series 566,American Chemical Society, Washington, D.C., chapter 15; Gong, C. S.,Cao, N. J., Du, J., and Tsao, G. T., 1999, Ethanol production fromrenewable resources, in Advances in BiochemicalEngineering/Biotechnology, Scheper, T., ed., Springer-Verlag BerlinHeidelberg, Germany, 65: 207-241; Olsson and Hahn-Hagerdal, 1996,Fermentation of lignocellulosic hydrolysates for ethanol production,Enz. Microb. Tech. 18: 312-331; and Vallander and Eriksson, 1990,Production of ethanol from lignocellulosic materials: State of the art,Adv. Biochem. Eng./Biotechnol. 42: 63-95).

Saccharification.

In the hydrolysis step, also known as saccharification, the cellulosicor xylan-containing material, e.g., pretreated, is hydrolyzed to breakdown cellulose and/or hemicellulose to fermentable sugars, such asglucose, cellobiose, xylose, xylulose, arabinose, mannose, galactose,and/or soluble oligosaccharides. The hydrolysis is performedenzymatically by an enzyme composition as described herein in thepresence of a polypeptide having cellobiohydrolase, endoglucanase,cellulolytic enhancing, or xylanase activity of the present invention.The enzyme components of the compositions can be added simultaneously orsequentially.

Enzymatic hydrolysis is preferably carried out in a suitable aqueousenvironment under conditions that can be readily determined by oneskilled in the art. In one aspect, hydrolysis is performed underconditions suitable for the activity of the enzyme components, i.e.,optimal for the enzyme components. The hydrolysis can be carried out asa fed batch or continuous process where the cellulosic orxylan-containing material is fed gradually to, for example, an enzymecontaining hydrolysis solution.

The saccharification is generally performed in stirred-tank reactors orfermentors under controlled pH, temperature, and mixing conditions.Suitable process time, temperature and pH conditions can readily bedetermined by one skilled in the art. For example, the saccharificationcan last up to 200 hours, but is typically performed for preferablyabout 12 to about 120 hours, e.g., about 16 to about 72 hours or about24 to about 48 hours. The temperature is in the range of preferablyabout 25° C. to about 70° C., e.g., about 30° C. to about 65° C., about40° C. to about 60° C., or about 50° C. to about 55° C. The pH is in therange of preferably about 3 to about 8, e.g., about 3.5 to about 7,about 4 to about 6, or about 5.0 to about 5.5. The dry solids content isin the range of preferably about 5 to about 50 wt %, e.g., about 10 toabout 40 wt % or about 20 to about 30 wt %.

The enzyme compositions can comprise any protein useful in degrading orconverting the cellulosic or xylan-containing material.

In one aspect, the enzyme composition comprises or further comprises oneor more (e.g., several) proteins selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, an expansin, a laccase, a ligninolyticenzyme, a pectinase, a peroxidase, a protease, and a swollenin. Inanother aspect, the cellulase is preferably one or more (e.g., several)enzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase. In another aspect, thehemicellulase is preferably one or more (e.g., several) enzymes selectedfrom the group consisting of an acetylmannan esterase, an acetylxylanesterase, an arabinanase, an arabinofuranosidase, a coumaric acidesterase, a feruloyl esterase, a galactosidase, a glucuronidase, aglucuronoyl esterase, a mannanase, a mannosidase, a xylanase, and axylosidase.

In another aspect, the enzyme composition comprises one or more (e.g.,several) cellulolytic enzymes. In another aspect, the enzyme compositioncomprises or further comprises one or more (e.g., several)hemicellulolytic enzymes. In another aspect, the enzyme compositioncomprises one or more (e.g., several) cellulolytic enzymes and one ormore (e.g., several) hemicellulolytic enzymes. In another aspect, theenzyme composition comprises one or more (e.g., several) enzymesselected from the group of cellulolytic enzymes and hemicellulolyticenzymes. In another aspect, the enzyme composition comprises anendoglucanase. In another aspect, the enzyme composition comprises acellobiohydrolase. In another aspect, the enzyme composition comprises abeta-glucosidase. In another aspect, the enzyme composition comprises apolypeptide having cellulolytic enhancing activity. In another aspect,the enzyme composition comprises an endoglucanase and a polypeptidehaving cellulolytic enhancing activity. In another aspect, the enzymecomposition comprises a cellobiohydrolase and a polypeptide havingcellulolytic enhancing activity. In another aspect, the enzymecomposition comprises a beta-glucosidase and a polypeptide havingcellulolytic enhancing activity. In another aspect, the enzymecomposition comprises an endoglucanase and a cellobiohydrolase. Inanother aspect, the enzyme composition comprises an endoglucanase and abeta-glucosidase. In another aspect, the enzyme composition comprises acellobiohydrolase and a beta-glucosidase. In another aspect, the enzymecomposition comprises an endoglucanase, a cellobiohydrolase, and apolypeptide having cellulolytic enhancing activity. In another aspect,the enzyme composition comprises an endoglucanase, a beta-glucosidase,and a polypeptide having cellulolytic enhancing activity. In anotheraspect, the enzyme composition comprises a cellobiohydrolase, abeta-glucosidase, and a polypeptide having cellulolytic enhancingactivity. In another aspect, the enzyme composition comprises anendoglucanase, a cellobiohydrolase, and a beta-glucosidase. In anotheraspect, the enzyme composition comprises an endoglucanase, acellobiohydrolase, a beta-glucosidase, and a polypeptide havingcellulolytic enhancing activity.

In another aspect, the enzyme composition comprises an acetylmannanesterase. In another aspect, the enzyme composition comprises anacetylxylan esterase. In another aspect, the enzyme compositioncomprises an arabinanase (e.g., alpha-L-arabinanase). In another aspect,the enzyme composition comprises an arabinofuranosidase (e.g.,alpha-L-arabinofuranosidase). In another aspect, the enzyme compositioncomprises a coumaric acid esterase. In another aspect, the enzymecomposition comprises a feruloyl esterase. In another aspect, the enzymecomposition comprises a galactosidase (e.g., alpha-galactosidase and/orbeta-galactosidase). In another aspect, the enzyme composition comprisesa glucuronidase (e.g., alpha-D-glucuronidase). In another aspect, theenzyme composition comprises a glucuronoyl esterase. In another aspect,the enzyme composition comprises a mannanase. In another aspect, theenzyme composition comprises a mannosidase (e.g., beta-mannosidase). Inanother aspect, the enzyme composition comprises a xylanase. In apreferred aspect, the xylanase is a Family 10 xylanase. In anotheraspect, the enzyme composition comprises a xylosidase (e.g.,beta-xylosidase).

In another aspect, the enzyme composition comprises an esterase. Inanother aspect, the enzyme composition comprises an expansin. In anotheraspect, the enzyme composition comprises a laccase. In another aspect,the enzyme composition comprises a ligninolytic enzyme. In a preferredaspect, the ligninolytic enzyme is a manganese peroxidase. In anotherpreferred aspect, the ligninolytic enzyme is a lignin peroxidase. Inanother preferred aspect, the ligninolytic enzyme is a H₂O₂-producingenzyme. In another aspect, the enzyme composition comprises a pectinase.In another aspect, the enzyme composition comprises a peroxidase. Inanother aspect, the enzyme composition comprises a protease. In anotheraspect, the enzyme composition comprises a swollenin

In the processes of the present invention, the enzyme(s) can be addedprior to or during saccharification, saccharification and fermentation,or fermentation.

One or more (e.g., several) components of the enzyme composition may bewild-type proteins, recombinant proteins, or a combination of wild-typeproteins and recombinant proteins. For example, one or more (e.g.,several) components may be native proteins of a cell, which is used as ahost cell to express recombinantly one or more (e.g., several) othercomponents of the enzyme composition. One or more (e.g., several)components of the enzyme composition may be produced as monocomponents,which are then combined to form the enzyme composition. The enzymecomposition may be a combination of multicomponent and monocomponentprotein preparations.

The enzymes used in the processes of the present invention may be in anyform suitable for use, such as, for example, a fermentation brothformulation or a cell composition, a cell lysate with or withoutcellular debris, a semi-purified or purified enzyme preparation, or ahost cell as a source of the enzymes. The enzyme composition may be adry powder or granulate, a non-dusting granulate, a liquid, a stabilizedliquid, or a stabilized protected enzyme. Liquid enzyme preparationsmay, for instance, be stabilized by adding stabilizers such as a sugar,a sugar alcohol or another polyol, and/or lactic acid or another organicacid according to established processes.

The optimum amounts of the enzymes and polypeptides havingcellobiohydrolase, endoglucanase, cellulolytic enhancing, or xylanaseactivity depend on several factors including, but not limited to, themixture of cellulolytic and/or hemicellulolytic enzyme components, thecellulosic or xylan-containing material, the concentration of cellulosicor xylan-containing material, the pretreatment(s) of the cellulosic orxylan-containing material, temperature, time, pH, and inclusion offermenting organism (e.g., yeast for Simultaneous Saccharification andFermentation).

In one aspect, an effective amount of cellulolytic or hemicellulolyticenzyme to the cellulosic or xylan-containing material is about 0.5 toabout 50 mg, e.g., about 0.5 to about 40 mg, about 0.5 to about 25 mg,about 0.75 to about 20 mg, about 0.75 to about 15 mg, about 0.5 to about10 mg, or about 2.5 to about 10 mg per g of the cellulosic orxylan-containing material.

In another aspect, an effective amount of a polypeptide havingcellobiohydrolase, endoglucanase, cellulolytic enhancing, or xylanaseactivity to the cellulosic or xylan-containing material is about 0.01 toabout 50.0 mg, e.g., about 0.01 to about 40 mg, about 0.01 to about 30mg, about 0.01 to about 20 mg, about 0.01 to about 10 mg, about 0.01 toabout 5 mg, about 0.025 to about 1.5 mg, about 0.05 to about 1.25 mg,about 0.075 to about 1.25 mg, about 0.1 to about 1.25 mg, about 0.15 toabout 1.25 mg, or about 0.25 to about 1.0 mg per g of the cellulosic orxylan-containing material.

In another aspect, an effective amount of a polypeptide havingcellobiohydrolase, endoglucanase, cellulolytic enhancing, or xylanaseactivity to cellulolytic or hemicellulolytic enzyme is about 0.005 toabout 1.0 g, e.g., about 0.01 to about 1.0 g, about 0.15 to about 0.75g, about 0.15 to about 0.5 g, about 0.1 to about 0.5 g, about 0.1 toabout 0.25 g, or about 0.05 to about 0.2 g per g of cellulolytic orhemicellulolytic enzyme.

The polypeptides having cellulolytic enzyme activity or hemicellulolyticenzyme activity as well as other proteins/polypeptides useful in thedegradation of the cellulosic or xylan-containing material, e.g., GH61polypeptides having cellulolytic enhancing activity (collectivelyhereinafter “polypeptides having enzyme activity”) can be derived orobtained from any suitable origin, including, bacterial, fungal, yeast,plant, or mammalian origin. The term “obtained” also means herein thatthe enzyme may have been produced recombinantly in a host organismemploying methods described herein, wherein the recombinantly producedenzyme is either native or foreign to the host organism or has amodified amino acid sequence, e.g., having one or more (e.g., several)amino acids that are deleted, inserted and/or substituted, i.e., arecombinantly produced enzyme that is a mutant and/or a fragment of anative amino acid sequence or an enzyme produced by nucleic acidshuffling processes known in the art. Encompassed within the meaning ofa native enzyme are natural variants and within the meaning of a foreignenzyme are variants obtained recombinantly, such as by site-directedmutagenesis or shuffling.

A polypeptide having enzyme activity may be a bacterial polypeptide. Forexample, the polypeptide may be a Gram-positive bacterial polypeptidesuch as a Bacillus, Streptococcus, Streptomyces, Staphylococcus,Enterococcus, Lactobacillus, Lactococcus, Clostridium, Geobacillus,Caldicellulosiruptor, Acidothermus, Thermobifidia, or Oceanobacilluspolypeptide having enzyme activity, or a Gram negative bacterialpolypeptide such as an E. coli, Pseudomonas, Salmonella, Campylobacter,Helicobacter, Flavobacterium, Fusobacterium, Ilyobacter, Neisseria, orUreaplasma polypeptide having enzyme activity.

In one aspect, the polypeptide is a Bacillus alkalophilus, Bacillusamyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillusclausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacilluslentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus,Bacillus stearothermophilus, Bacillus subtilis, or Bacillusthuringiensis polypeptide having enzyme activity.

In another aspect, the polypeptide is a Streptococcus equisimilis,Streptococcus pyogenes, Streptococcus uberis, or Streptococcus equisubsp. Zooepidemicus polypeptide having enzyme activity.

In another aspect, the polypeptide is a Streptomyces achromogenes,Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus,or Streptomyces lividans polypeptide having enzyme activity.

The polypeptide having enzyme activity may also be a fungal polypeptide,and more preferably a yeast polypeptide such as a Candida,Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, or Yarrowiapolypeptide having enzyme activity; or more preferably a filamentousfungal polypeptide such as an Acremonium, Agaricus, Alternaria,Aspergillus, Aureobasidium, Botryosphaeria, Ceriporiopsis, Chaetomidium,Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes,Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium,Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula,Leptospaeria, Magnaporthe, Melanocarpus, Meripilus, Mucor,Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium,Phanerochaete, Piromyces, Poitrasia, Pseudoplectania,Pseudotrichonympha, Rhizomucor, Schizophyllum, Scytalidium, Talaromyces,Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea,Verticillium, Volvariella, or Xylaria polypeptide having enzymeactivity.

In one aspect, the polypeptide is a Saccharomyces carlsbergensis,Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomycesdouglasii, Saccharomyces kluyveri, Saccharomyces norbensis, orSaccharomyces oviformis polypeptide having enzyme activity.

In another aspect, the polypeptide is an Acremonium cellulolyticus,Aspergillus aculeatus, Aspergillus awamori, Aspergillus fumigatus,Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans,Aspergillus niger, Aspergillus oryzae, Chrysosporium keratinophilum,Chrysosporium lucknowense, Chrysosporium tropicum, Chrysosporiummerdarium, Chrysosporium inops, Chrysosporium pannicola, Chrysosporiumqueenslandicum, Chrysosporium zonatum, Fusarium bactridioides, Fusariumcerealis, Fusarium crookwellense, Fusarium culmorum, Fusariumgraminearum, Fusarium graminum, Fusarium heterosporum, Fusarium negundi,Fusarium oxysporum, Fusarium reticulatum, Fusarium roseum, Fusariumsambucinum, Fusarium sarcochroum, Fusarium sporotrichioides, Fusariumsulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusariumvenenatum, Humicola grisea, Humicola insolens, Humicola lanuginosa,Irpex lacteus, Mucor miehei, Myceliophthora thermophila, Neurosporacrassa, Penicillium funiculosum, Penicillium purpurogenum, Phanerochaetechrysosporium, Thielavia achromatica, Thielavia albomyces, Thielaviaalbopilosa, Thielavia austra/einsis, Thielavia fimeti, Thielaviamicrospora, Thielavia ovispora, Thielavia peruviana, Thielaviaspededonium, Thielavia setosa, Thielavia subthermophila, Thielaviaterrestris, Trichoderma harzianum, Trichoderma koningii, Trichodermalongibrachiatum, Trichoderma reesei, Trichoderma viride, or Trichophaeasaccata polypeptide having enzyme activity.

Chemically modified or protein engineered mutants of polypeptides havingenzyme activity may also be used.

One or more (e.g., several) components of the enzyme composition may bea recombinant component, i.e., produced by cloning of a DNA sequenceencoding the single component and subsequent cell transformed with theDNA sequence and expressed in a host (see, for example, WO 91/17243 andWO 91/17244). The host is preferably a heterologous host (enzyme isforeign to host), but the host may under certain conditions also be ahomologous host (enzyme is native to host). Monocomponent cellulolyticproteins may also be prepared by purifying such a protein from afermentation broth.

In one aspect, the one or more (e.g., several) cellulolytic enzymescomprise a commercial cellulolytic enzyme preparation. Examples ofcommercial cellulolytic enzyme preparations suitable for use in thepresent invention include, for example, CELLIC® CTec (Novozymes A/S),CELLIC® CTec2 (Novozymes A/S), CELLUCLAST™ (Novozymes A/S), NOVOZYM™ 188(Novozymes A/S), CELLUZYME™ (Novozymes A/S), CEREFLO™ (Novozymes A/S),and ULTRAFLO™ (Novozymes A/S), ACCELERASE™ (Genencor Int.), LAMI NEXT′″(Genencor Int.), SPEZYME™ CP (Genencor Int.), FILTRASE® NL (DSM);METHAPLUS® S/L 100 (DSM), ROHAMENT™ 7069 W (Röhm GmbH), FIBREZYME® LDI(Dyadic International, Inc.), FIBREZYME® LBR (Dyadic International,Inc.), or VISCOSTAR® 150L (Dyadic International, Inc.). The cellulaseenzymes are added in amounts effective from about 0.001 to about 5.0 wt% of solids, e.g., about 0.025 to about 4.0 wt % of solids or about0.005 to about 2.0 wt % of solids.

Examples of bacterial endoglucanases that can be used in the processesof the present invention, include, but are not limited to, anAcidothermus cellulolyticus endoglucanase (WO 91/05039; WO 93/15186;U.S. Pat. No. 5,275,944; WO 96/02551; U.S. Pat. No. 5,536,655, WO00/70031, WO 05/093050); Thermobifida fusca endoglucanase III (WO05/093050); and Thermobifida fusca endoglucanase V (WO 05/093050).

Examples of fungal endoglucanases that can be used in the presentinvention, include, but are not limited to, a Trichoderma reeseiendoglucanase I (Penttila et al., 1986, Gene 45: 253-263, Trichodermareesei Cel7B endoglucanase I (GENBANK™ accession no. M15665),Trichoderma reesei endoglucanase II (Saloheimo, et al., 1988, Gene63:11-22), Trichoderma reesei Cel5A endoglucanase II (GENBANK™ accessionno. M19373), Trichoderma reesei endoglucanase III (Okada et al., 1988,Appl. Environ. Microbiol. 64: 555-563, GENBANK™ accession no. AB003694),Trichoderma reesei endoglucanase V (Saloheimo et al., 1994, MolecularMicrobiology 13: 219-228, GENBANK™ accession no. Z33381), Aspergillusaculeatus endoglucanase (Ooi et al., 1990, Nucleic Acids Research 18:5884), Aspergillus kawachii endoglucanase (Sakamoto et al., 1995,Current Genetics 27: 435-439), Erwinia carotovara endoglucanase(Saarilahti et al., 1990, Gene 90: 9-14), Fusarium oxysporumendoglucanase (GENBANK™ accession no. L29381), Humicola grisea var.thermoidea endoglucanase (GENBANK™ accession no. AB003107), Melanocarpusalbomyces endoglucanase (GENBANK™ accession no. MAL515703), Neurosporacrassa endoglucanase (GENBANK™ accession no. XM_324477), Humicolainsolens endoglucanase V, Myceliophthora thermophila CBS 117.65endoglucanase, basidiomycete CBS 495.95 endoglucanase, basidiomycete CBS494.95 endoglucanase, Thielavia terrestris NRRL 8126 CEL6Bendoglucanase, Thielavia terrestris NRRL 8126 CEL6C endoglucanase,Thielavia terrestris NRRL 8126 CEL7C endoglucanase, Thielavia terrestrisNRRL 8126 CEL7E endoglucanase, Thielavia terrestris NRRL 8126 CEL7Fendoglucanase, Cladorrhinum foecundissimum ATCC 62373 CEL7Aendoglucanase, and Trichoderma reesei strain No. VTT-D-80133endoglucanase (GENBANK™ accession no. M15665).

Examples of cellobiohydrolases useful in the present invention include,but are not limited to, Aspergillus aculeatus cellobiohydrolase II (WO2011/059740), Chaetomium thermophilum cellobiohydrolase I, Chaetomiumthermophilum cellobiohydrolase II, Humicola insolens cellobiohydrolaseI, Myceliophthora thermophila cellobiohydrolase II (WO 2009/042871),Thielavia hyrcanie cellobiohydrolase II (WO 2010/141325), Thielaviaterrestris cellobiohydrolase II (CEL6A, WO 2006/074435), Trichodermareesei cellobiohydrolase I, Trichoderma reesei cellobiohydrolase II, andTrichophaea saccata cellobiohydrolase II (WO 2010/057086).

Examples of beta-glucosidases useful in the present invention include,but are not limited to, beta-glucosidases from Aspergillus aculeatus(Kawaguchi et al., 1996, Gene 173: 287-288), Aspergillus fumigatus (WO2005/047499), Aspergillus niger (Dan et al., 2000, J. Biol. Chem. 275:4973-4980), Aspergillus oryzae (WO 2002/095014), Penicillium brasilianumIBT 20888 (WO 2007/019442 and WO 2010/088387), Thielavia terrestris (WO2011/035029), and Trichophaea saccata (WO 2007/019442).

The beta-glucosidase may be a fusion protein. In one aspect, thebeta-glucosidase is an Aspergillus oryzae beta-glucosidase variant BGfusion protein (WO 2008/057637) or an Aspergillus oryzaebeta-glucosidase fusion protein (WO 2008/057637.

Other useful endoglucanases, cellobiohydrolases, and beta-glucosidasesare disclosed in numerous Glycosyl Hydrolase families using theclassification according to Henrissat B., 1991, A classification ofglycosyl hydrolases based on amino-acid sequence similarities, Biochem.J. 280: 309-316, and Henrissat B., and Bairoch A., 1996, Updating thesequence-based classification of glycosyl hydrolases, Biochem. J. 316:695-696.

Other cellulolytic enzymes that may be used in the present invention aredescribed in WO 98/13465, WO 98/015619, WO 98/015633, WO 99/06574, WO99/10481, WO 99/025847, WO 99/031255, WO 2002/101078, WO 2003/027306, WO2003/052054, WO 2003/052055, WO 2003/052056, WO 2003/052057, WO2003/052118, WO 2004/016760, WO 2004/043980, WO 2004/048592, WO2005/001065, WO 2005/028636, WO 2005/093050, WO 2005/093073, WO2006/074005, WO 2006/117432, WO 2007/071818, WO 2007/071820, WO2008/008070, WO 2008/008793, U.S. Pat. Nos. 5,457,046, 5,648,263, and5,686,593.

In the processes of the present invention, any GH61 polypeptide havingcellulolytic enhancing activity can be used as a component of the enzymecomposition.

Examples of GH61 polypeptides having cellulolytic enhancing activityuseful in the processes of the present invention include, but are notlimited to, GH61 polypeptides from Thielavia terrestris (WO 2005/074647,WO 2008/148131, and WO 2011/035027), Thermoascus aurantiacus (WO2005/074656 and WO 2010/065830), Trichoderma reesei (WO 2007/089290),Myceliophthora thermophila (WO 2009/085935, WO 2009/085859, WO2009/085864, WO 2009/085868), Aspergillus fumigatus (WO 2010/138754),GH61 polypeptides from Penicillium pinophilum (WO 2011/005867),Thermoascus sp. (WO 2011/039319), Penicillium sp. (WO 2011/041397), andThermoascus crustaceous (WO 2011/041504).

In one aspect, the GH61 polypeptide having cellulolytic enhancingactivity is used in the presence of a soluble activating divalent metalcation according to WO 2008/151043, e.g., manganese or copper sulfate.

In another aspect, the GH61 polypeptide having cellulolytic enhancingactivity is used in the presence of a dioxy compound, a bicyliccompound, a heterocyclic compound, a nitrogen-containing compound, aquinone compound, a sulfur-containing compound, or a liquor obtainedfrom a pretreated cellulosic material such as pretreated corn stover(PCS).

The dioxy compound may include any suitable compound containing two ormore oxygen atoms. In some aspects, the dioxy compounds contain asubstituted aryl moiety as described herein. The dioxy compounds maycomprise one or more (e.g., several) hydroxyl and/or hydroxylderivatives, but also include substituted aryl moieties lacking hydroxyland hydroxyl derivatives. Non-limiting examples of the dioxy compoundsinclude pyrocatechol or catechol; caffeic acid; 3,4-dihydroxybenzoicacid; 4-tert-butyl-5-methoxy-1,2-benzenediol; pyrogallol; gallic acid;methyl-3,4,5-trihydroxybenzoate; 2,3,4-trihydroxybenzophenone;2,6-dimethoxyphenol; sinapinic acid; 3,5-dihydroxybenzoic acid;4-chloro-1,2-benzenediol; 4-nitro-1,2-benzenediol; tannic acid; ethylgallate; methyl glycolate; dihydroxyfumaric acid; 2-butyne-1,4-diol;(croconic acid; 1,3-propanediol; tartaric acid; 2,4-pentanediol;3-ethyoxy-1,2-propanediol; 2,4,4′-trihydroxybenzophenone;cis-2-butene-1,4-diol; 3,4-dihydroxy-3-cyclobutene-1,2-dione;dihydroxyacetone; acrolein acetal; methyl-4-hydroxybenzoate;4-hydroxybenzoic acid; and methyl-3,5-dimethoxy-4-hydroxybenzoate; or asalt or solvate thereof.

The bicyclic compound may include any suitable substituted fused ringsystem as described herein. The compounds may comprise one or more(e.g., several) additional rings, and are not limited to a specificnumber of rings unless otherwise stated. In one aspect, the bicycliccompound is a flavonoid. In another aspect, the bicyclic compound is anoptionally substituted isoflavonoid. In another aspect, the bicycliccompound is an optionally substituted flavylium ion, such as anoptionally substituted anthocyanidin or optionally substitutedanthocyanin, or derivative thereof. Non-limiting examples of thebicyclic compounds include epicatechin; quercetin; myricetin; taxifolin;kaempferol; morin; acacetin; naringenin; isorhamnetin; apigenin;cyanidin; cyanin; kuromanin; keracyanin; or a salt or solvate thereof.

The heterocyclic compound may be any suitable compound, such as anoptionally substituted aromatic or non-aromatic ring comprising aheteroatom, as described herein. In one aspect, the heterocyclic is acompound comprising an optionally substituted heterocycloalkyl moiety oran optionally substituted heteroaryl moiety. In another aspect, theoptionally substituted heterocycloalkyl moiety or optionally substitutedheteroaryl moiety is an optionally substituted 5-memberedheterocycloalkyl or an optionally substituted 5-membered heteroarylmoiety. In another aspect, the optionally substituted heterocycloalkylor optionally substituted heteroaryl moiety is an optionally substitutedmoiety selected from pyrazolyl, furanyl, imidazolyl, isoxazolyl,oxadiazolyl, oxazolyl, pyrrolyl, pyridyl, pyrimidyl, pyridazinyl,thiazolyl, triazolyl, thienyl, dihydrothieno-pyrazolyl, thianaphthenyl,carbazolyl, benzimidazolyl, benzothienyl, benzofuranyl, indolyl,quinolinyl, benzotriazolyl, benzothiazolyl, benzooxazolyl,benzimidazolyl, isoquinolinyl, isoindolyl, acridinyl, benzoisazolyl,dimethylhydantoin, pyrazinyl, tetrahydrofuranyl, pyrrolinyl,pyrrolidinyl, morpholinyl, indolyl, diazepinyl, azepinyl, thiepinyl,piperidinyl, and oxepinyl. In another aspect, the optionally substitutedheterocycloalkyl moiety or optionally substituted heteroaryl moiety isan optionally substituted furanyl. Non-limiting examples of theheterocyclic compounds include(1,2-dihydroxyethyl)-3,4-dihydroxyfuran-2(5H)-one;4-hydroxy-5-methyl-3-furanone; 5-hydroxy-2(5H)-furanone;[1,2-dihydroxyethyl]furan-2,3,4(5H)-trione; α-hydroxy-γ-butyrolactone;ribonic γ-lactone; aldohexuronicaldohexuronic acid γ-lactone; gluconicacid δ-lactone; 4-hydroxycoumarin; dihydrobenzofuran;5-(hydroxymethyl)furfural; furoin; 2(5H)-furanone;5,6-dihydro-2H-pyran-2-one; and5,6-dihydro-4-hydroxy-6-methyl-2H-pyran-2-one; or a salt or solvatethereof.

The nitrogen-containing compound may be any suitable compound with oneor more nitrogen atoms. In one aspect, the nitrogen-containing compoundcomprises an amine, imine, hydroxylamine, or nitroxide moiety.Non-limiting examples of the nitrogen-containing compounds includeacetone oxime; violuric acid; pyridine-2-aldoxime; 2-aminophenol;1,2-benzenediamine; 2,2,6,6-tetramethyl-1-piperidinyloxy;5,6,7,8-tetrahydrobiopterin; 6,7-dimethyl-5,6,7,8-tetrahydropterine; andmaleamic acid; or a salt or solvate thereof.

The quinone compound may be any suitable compound comprising a quinonemoiety as described herein. Non-limiting examples of the quinonecompounds include 1,4-benzoquinone; 1,4-naphthoquinone;2-hydroxy-1,4-naphthoquinone; 2,3-dimethoxy-5-methyl-1,4-benzoquinone orcoenzyme Q₀; 2,3,5,6-tetramethyl-1,4-benzoquinone or duroquinone;1,4-dihydroxyanthraquinone; 3-hydroxy-1-methyl-5,6-indolinedione oradrenochrome; 4-tert-butyl-5-methoxy-1,2-benzoquinone; pyrroloquinolinequinone; or a salt or solvate thereof.

The sulfur-containing compound may be any suitable compound comprisingone or more sulfur atoms. In one aspect, the sulfur-containing comprisesa moiety selected from thionyl, thioether, sulfinyl, sulfonyl,sulfamide, sulfonamide, sulfonic acid, and sulfonic ester. Non-limitingexamples of the sulfur-containing compounds include ethanethiol;2-propanethiol; 2-propene-1-thiol; 2-mercaptoethanesulfonic acid;benzenethiol; benzene-1,2-dithiol; cysteine; methionine; glutathione;cystine; or a salt or solvate thereof.

In one aspect, an effective amount of such a compound described above tocellulosic material as a molar ratio to glucosyl units of cellulose isabout 10⁻⁶ to about 10, e.g., about 10⁻⁶ to about 7.5, about 10⁻⁶ toabout 5, about 10⁻⁶ to about 2.5, about 10⁻⁶ to about 1, about 10⁻⁵ toabout 1, about 10⁻⁵ to about 10⁻¹, about 10⁻⁴ to about 10⁻¹, about 10⁻³to about 10⁻¹, or about 10⁻³ to about 10⁻². In another aspect, aneffective amount of such a compound described above is about 0.1 μM toabout 1 M, e.g., about 0.5 μM to about 0.75 M, about 0.75 μM to about0.5 M, about 1 μM to about 0.25 M, about 1 μM to about 0.1 M, about 5 μMto about 50 mM, about 10 μM to about 25 mM, about 50 μM to about 25 mM,about 10 μM to about 10 mM, about 5 μM to about 5 mM, or about 0.1 mM toabout 1 mM.

The term “liquor” means the solution phase, either aqueous, organic, ora combination thereof, arising from treatment of a lignocellulose and/orhemicellulose material in a slurry, or monosaccharides thereof, e.g.,xylose, arabinose, mannose, etc., under conditions as described herein,and the soluble contents thereof. A liquor for cellulolytic enhancementof a GH61 polypeptide can be produced by treating a lignocellulose orhemicellulose material (or feedstock) by applying heat and/or pressure,optionally in the presence of a catalyst, e.g., acid, optionally in thepresence of an organic solvent, and optionally in combination withphysical disruption of the material, and then separating the solutionfrom the residual solids. Such conditions determine the degree ofcellulolytic enhancement obtainable through the combination of liquorand a GH61 polypeptide during hydrolysis of a cellulosic substrate by acellulase preparation. The liquor can be separated from the treatedmaterial using a method standard in the art, such as filtration,sedimentation, or centrifugation.

In one aspect, an effective amount of the liquor to cellulose is about10⁻⁶ to about 10 g per g of cellulose, e.g., about 10⁻⁶ to about 7.5 g,about 10⁻⁶ to about 5, about 10⁻⁶ to about 2.5 g, about 10⁻⁶ to about 1g, about 10⁻⁵ to about 1 g, about 10⁻⁵ to about 10⁻¹ g, about 10⁻⁴ toabout 10⁻¹ g, about 10⁻³ to about 10⁻¹ g, or about 10⁻³ to about 10⁻² gper g of cellulose.

In one aspect, the one or more (e.g., several) hemicellulolytic enzymescomprise a commercial hemicellulolytic enzyme preparation. Examples ofcommercial hemicellulolytic enzyme preparations suitable for use in thepresent invention include, for example, SHEARZYME™ (Novozymes A/S),CELLIC® HTec (Novozymes A/S), CELLIC® HTec2 (Novozymes A/S), VISCOZYME®(Novozymes A/S), ULTRAFLO® (Novozymes A/S), PULPZYME® HC (NovozymesA/S), MULTIFECT® Xylanase (Genencor), ACCELLERASE® XY (Genencor),ACCELLERASE® XC (Genencor), ECOPULP® TX-200A (AB Enzymes), HSP 6000Xylanase (DSM), DEPOL™ 333P (Biocatalysts Limit, Wales, UK), DEPOL™740L. (Biocatalysts Limit, Wales, UK), and DEPOL™ 762P (BiocatalystsLimit, Wales, UK).

Examples of xylanases useful in the processes of the present inventioninclude, but are not limited to, xylanases from Aspergillus aculeatus(GeneSeqP:AAR63790; WO 94/21785), Aspergillus fumigatus (WO2006/078256), Penicillium pinophilum (WO 2011/041405), Penicillium sp.(WO 2010/126772), Thielavia terrestris NRRL 8126 (WO 2009/079210), andTrichophaea saccata GH10 (WO 2011/057083).

Examples of beta-xylosidases useful in the processes of the presentinvention include, but are not limited to, beta-xylosidases fromNeurospora crassa (SwissProt accession number Q7SOW4), Trichodermareesei (UniProtKB/TrEMBL accession number Q92458), and Talaromycesemersonii (SwissProt accession number Q8X212).

Examples of acetylxylan esterases useful in the processes of the presentinvention include, but are not limited to, acetylxylan esterases fromAspergillus aculeatus (WO 2010/108918), Chaetomium globosum (Uniprotaccession number Q2GWX4), Chaetomium gracile (GeneSeqP accession numberAAB82124), Humicola insolens DSM 1800 (WO 2009/073709), Hypocreajecorina (WO 2005/001036), Myceliophtera thermophila (WO 2010/014880),Neurospora crassa (UniProt accession number q7s259), Phaeosphaerianodorum (Uniprot accession number Q0UHJ1), and Thielavia terrestris NRRL8126 (WO 2009/042846).

Examples of feruloyl esterases (ferulic acid esterases) useful in theprocesses of the present invention include, but are not limited to,feruloyl esterases form Humicola insolens DSM 1800 (WO 2009/076122),Neosartorya fischeri (UniProt Accession number A1D9T4), Neurosporacrassa (UniProt accession number Q9HGR3), Penicillium aurantiogriseum(WO 2009/127729), and Thielavia terrestris (WO 2010/053838 and WO2010/065448).

Examples of arabinofuranosidases useful in the processes of the presentinvention include, but are not limited to, arabinofuranosidases fromAspergillus niger(GeneSeqP accession number AAR94170), Humicola insolensDSM 1800 (WO 2006/114094 and WO 2009/073383), and M. giganteus (WO2006/114094).

Examples of alpha-glucuronidases useful in the processes of the presentinvention include, but are not limited to, alpha-glucuronidases fromAspergillus clavatus (UniProt accession number alccl 2), Aspergillusfumigatus (SwissProt accession number Q4WW45), Aspergillus niger(Uniprot accession number Q96WX9), Aspergillus terreus (SwissProtaccession number Q0CJP9), Humicola insolens (WO 2010/014706),Penicillium aurantiogriseum (WO 2009/068565), Talaromyces emersonii(UniProt accession number Q8X211), and Trichoderma reesei (Uniprotaccession number Q99024).

The polypeptides having enzyme activity used in the processes of thepresent invention may be produced by fermentation of the above-notedmicrobial strains on a nutrient medium containing suitable carbon andnitrogen sources and inorganic salts, using procedures known in the art(see, e.g., Bennett, J. W. and LaSure, L. (eds.), More GeneManipulations in Fungi, Academic Press, C A, 1991). Suitable media areavailable from commercial suppliers or may be prepared according topublished compositions (e.g., in catalogues of the American Type CultureCollection). Temperature ranges and other conditions suitable for growthand enzyme production are known in the art (see, e.g., Bailey, J. E.,and Ollis, D. F., Biochemical Engineering Fundamentals, McGraw-Hill BookCompany, N Y, 1986).

The fermentation can be any method of cultivation of a cell resulting inthe expression or isolation of an enzyme or protein. Fermentation may,therefore, be understood as comprising shake flask cultivation, orsmall- or large-scale fermentation (including continuous, batch,fed-batch, or solid state fermentations) in laboratory or industrialfermentors performed in a suitable medium and under conditions allowingthe enzyme to be expressed or isolated. The resulting enzymes producedby the methods described above may be recovered from the fermentationmedium and purified by conventional procedures.

Fermentation.

The fermentable sugars obtained from the hydrolyzed cellulosic orxylan-containing material can be fermented by one or more (e.g.,several) fermenting microorganisms capable of fermenting the sugarsdirectly or indirectly into a desired fermentation product.“Fermentation” or “fermentation process” refers to any fermentationprocess or any process comprising a fermentation step. Fermentationprocesses also include fermentation processes used in the consumablealcohol industry (e.g., beer and wine), dairy industry (e.g., fermenteddairy products), leather industry, and tobacco industry. Thefermentation conditions depend on the desired fermentation product andfermenting organism and can easily be determined by one skilled in theart.

In the fermentation step, sugars, released from the cellulosic orxylan-containing material as a result of the pretreatment and enzymatichydrolysis steps, are fermented to a product, e.g., ethanol, by afermenting organism, such as yeast. Hydrolysis (saccharification) andfermentation can be separate or simultaneous, as described herein.

Any suitable hydrolyzed cellulosic or xylan-containing material can beused in the fermentation step in practicing the present invention. Thematerial is generally selected based on the desired fermentationproduct, i.e., the substance to be obtained from the fermentation, andthe process employed, as is well known in the art.

The term “fermentation medium” is understood herein to refer to a mediumbefore the fermenting microorganism(s) is(are) added, such as, a mediumresulting from a saccharification process, as well as a medium used in asimultaneous saccharification and fermentation process (SSF).

“Fermenting microorganism” refers to any microorganism, includingbacterial and fungal organisms, suitable for use in a desiredfermentation process to produce a fermentation product. The fermentingorganism can be hexose and/or pentose fermenting organisms, or acombination thereof. Both hexose and pentose fermenting organisms arewell known in the art. Suitable fermenting microorganisms are able toferment, i.e., convert, sugars, such as glucose, xylose, xylulose,arabinose, maltose, mannose, galactose, and/or oligosaccharides,directly or indirectly into the desired fermentation product. Examplesof bacterial and fungal fermenting organisms producing ethanol aredescribed by Lin et al., 2006, Appl. Microbiol. Biotechnol. 69: 627-642.

Examples of fermenting microorganisms that can ferment hexose sugarsinclude bacterial and fungal organisms, such as yeast. Preferred yeastincludes strains of Candida, Kluyveromyces, and Saccharomyces, e.g.,Candida sonorensis, Kluyveromyces marxianus, and Saccharomycescerevisiae.

Examples of fermenting organisms that can ferment pentose sugars intheir native state include bacterial and fungal organisms, such as someyeast. Preferred xylose fermenting yeast include strains of Candida,preferably C. sheatae or C. sonorensis; and strains of Pichia,preferably P. stipitis, such as P. stipitis CBS 5773. Preferred pentosefermenting yeast include strains of Pachysolen, preferably P.tannophilus. Organisms not capable of fermenting pentose sugars, such asxylose and arabinose, may be genetically modified to do so by methodsknown in the art.

Examples of bacteria that can efficiently ferment hexose and pentose toethanol include, for example, Bacillus coagulans, Clostridiumacetobutylicum, Clostridium thermocellum, Clostridium phytofermentans,Geobacillus sp., Thermoanaerobacter saccharolyticum, and Zymomonasmobilis (Philippidis, 1996, supra).

Other fermenting organisms include strains of Bacillus, such as Bacilluscoagulans; Candida, such as C. sonorensis, C. methanosorbosa, C.diddensiae, C. parapsilosis, C. naedodendra, C. blankii, C.entomophilia, C. brassicae, C. pseudotropicalis, C. boidinii, C. utilis,and C. scehatae; Clostridium, such as C. acetobutylicum, C.thermocellum, and C. phytofermentans; E. coli, especially E. colistrains that have been genetically modified to improve the yield ofethanol; Geobacillus sp.; Hansenula, such as Hansenula anomala;Klebsiella, such as K. oxytoca; Kluyveromyces, such as K. marxianus, K.lactis, K. thermotolerans, and K. fragilis; Schizosaccharomyces, such asS. pombe; Thermoanaerobacter, such as Thermoanaerobactersaccharolyticum; and Zymomonas, such as Zymomonas mobilis.

In a preferred aspect, the yeast is a Bretannomyces. In a more preferredaspect, the yeast is Bretannomyces clausenii. In another preferredaspect, the yeast is a Candida. In another more preferred aspect, theyeast is Candida sonorensis. In another more preferred aspect, the yeastis Candida boidinii. In another more preferred aspect, the yeast isCandida blankii. In another more preferred aspect, the yeast is Candidabrassicae. In another more preferred aspect, the yeast is Candidadiddensii. In another more preferred aspect, the yeast is Candidaentomophilia. In another more preferred aspect, the yeast is Candidapseudotropicalis. In another more preferred aspect, the yeast is Candidascehatae. In another more preferred aspect, the yeast is Candida utilis.In another preferred aspect, the yeast is a Clavispora. In another morepreferred aspect, the yeast is Clavispora lusitaniae. In another morepreferred aspect, the yeast is Clavispora opuntiae. In another preferredaspect, the yeast is a Kluyveromyces. In another more preferred aspect,the yeast is Kluyveromyces fragilis. In another more preferred aspect,the yeast is Kluyveromyces marxianus. In another more preferred aspect,the yeast is Kluyveromyces thermotolerans. In another preferred aspect,the yeast is a Pachysolen. In another more preferred aspect, the yeastis Pachysolen tannophilus. In another preferred aspect, the yeast is aPichia. In another more preferred aspect, the yeast is a Pichiastipitis. In another preferred aspect, the yeast is a Saccharomyces spp.In a more preferred aspect, the yeast is Saccharomyces cerevisiae. Inanother more preferred aspect, the yeast is Saccharomyces distaticus. Inanother more preferred aspect, the yeast is Saccharomyces uvarum.

In a preferred aspect, the bacterium is a Bacillus. In a more preferredaspect, the bacterium is Bacillus coagulans. In another preferredaspect, the bacterium is a Clostridium. In another more preferredaspect, the bacterium is Clostridium acetobutylicum. In another morepreferred aspect, the bacterium is Clostridium phytofermentans. Inanother more preferred aspect, the bacterium is Clostridiumthermocellum. In another more preferred aspect, the bacterium isGeobacillus sp. In another more preferred aspect, the bacterium is aThermoanaerobacter. In another more preferred aspect, the bacterium isThermoanaerobacter saccharolyticum. In another preferred aspect, thebacterium is a Zymomonas. In another more preferred aspect, thebacterium is Zymomonas mobilis.

Commercially available yeast suitable for ethanol production include,e.g., BIOFERM™ AFT and XR (NABC—North American Bioproducts Corporation,GA, USA), ETHANOL RED™ yeast (Fermentis/Lesaffre, USA), FALI™(Fleischmann's Yeast, USA), FERMIOL™ (DSM Specialties), GERT STRAND™(Gert Strand AB, Sweden), and SUPERSTART™ and THERMOSACC™ fresh yeast(Ethanol Technology, WI, USA).

In a preferred aspect, the fermenting microorganism has been geneticallymodified to provide the ability to ferment pentose sugars, such asxylose utilizing, arabinose utilizing, and xylose and arabinoseco-utilizing microorganisms.

The cloning of heterologous genes into various fermenting microorganismshas led to the construction of organisms capable of converting hexosesand pentoses to ethanol (co-fermentation) (Chen and Ho, 1993, Cloningand improving the expression of Pichia stipitis xylose reductase gene inSaccharomyces cerevisiae, Appl. Biochem. Biotechnol. 39-40: 135-147; Hoet al., 1998, Genetically engineered Saccharomyces yeast capable ofeffectively cofermenting glucose and xylose, Appl. Environ. Microbiol.64: 1852-1859; Kotter and Ciriacy, 1993, Xylose fermentation bySaccharomyces cerevisiae, Appl. Microbiol. Biotechnol. 38: 776-783;Walfridsson et al., 1995, Xylose-metabolizing Saccharomyces cerevisiaestrains overexpressing the TKL1 and TALI genes encoding the pentosephosphate pathway enzymes transketolase and transaldolase, Appl.Environ. Microbiol. 61: 4184-4190; Kuyper et al., 2004, Minimalmetabolic engineering of Saccharomyces cerevisiae for efficientanaerobic xylose fermentation: a proof of principle, FEMS Yeast Research4: 655-664; Beall et al., 1991, Parametric studies of ethanol productionfrom xylose and other sugars by recombinant Escherichia coli, Biotech.Bioeng. 38: 296-303; Ingram et al., 1998, Metabolic engineering ofbacteria for ethanol production, Biotechnol. Bioeng. 58: 204-214; Zhanget al., 1995, Metabolic engineering of a pentose metabolism pathway inethanologenic Zymomonas mobilis, Science 267: 240-243; Deanda et al.,1996, Development of an arabinose-fermenting Zymomonas mobilis strain bymetabolic pathway engineering, Appl. Environ. Microbiol. 62: 4465-4470;WO 2003/062430, xylose isomerase).

In a preferred aspect, the genetically modified fermenting microorganismis Candida sonorensis. In another preferred aspect, the geneticallymodified fermenting microorganism is Escherichia coli. In anotherpreferred aspect, the genetically modified fermenting microorganism isKlebsiella oxytoca. In another preferred aspect, the geneticallymodified fermenting microorganism is Kluyveromyces marxianus. In anotherpreferred aspect, the genetically modified fermenting microorganism isSaccharomyces cerevisiae. In another preferred aspect, the geneticallymodified fermenting microorganism is Zymomonas mobilis.

It is well known in the art that the organisms described above can alsobe used to produce other substances, as described herein.

The fermenting microorganism is typically added to the degradedcellulosic or xylan-containing material or hydrolysate and thefermentation is performed for about 8 to about 96 hours, e.g., about 24to about 60 hours. The temperature is typically between about 26° C. toabout 60° C., e.g., about 32° C. or 50° C., and about pH 3 to about pH8, e.g., pH 4-5, 6, or 7.

In one aspect, the yeast and/or another microorganism are applied to thedegraded cellulosic or xylan-containing material and the fermentation isperformed for about 12 to about 96 hours, such as typically 24-60 hours.In another aspect, the temperature is preferably between about 20° C. toabout 60° C., e.g., about 25° C. to about 50° C., about 32° C. to about50° C., or about 32° C. to about 50° C., and the pH is generally fromabout pH 3 to about pH 7, e.g., about pH 4 to about pH 7. However, somefermenting organisms, e.g., bacteria, have higher fermentationtemperature optima. Yeast or another microorganism is preferably appliedin amounts of approximately 10⁵ to 10¹², preferably from approximately10⁷ to 10¹⁰, especially approximately 2×10⁸ viable cell count per ml offermentation broth. Further guidance in respect of using yeast forfermentation can be found in, e.g., “The Alcohol Textbook” (Editors K.Jacques, T. P. Lyons and D. R. Kelsall, Nottingham University Press,United Kingdom 1999), which is hereby incorporated by reference.

For ethanol production, following the fermentation the fermented slurryis distilled to extract the ethanol. The ethanol obtained according tothe processes of the invention can be used as, e.g., fuel ethanol,drinking ethanol, i.e., potable neutral spirits, or industrial ethanol.

A fermentation stimulator can be used in combination with any of theprocesses described herein to further improve the fermentation process,and in particular, the performance of the fermenting microorganism, suchas, rate enhancement and ethanol yield. A “fermentation stimulator”refers to stimulators for growth of the fermenting microorganisms, inparticular, yeast. Preferred fermentation stimulators for growth includevitamins and minerals. Examples of vitamins include multivitamins,biotin, pantothenate, nicotinic acid, meso-inositol, thiamine,pyridoxine, para-aminobenzoic acid, folic acid, riboflavin, and VitaminsA, B, C, D, and E. See, for example, Alfenore et al., Improving ethanolproduction and viability of Saccharomyces cerevisiae by a vitaminfeeding strategy during fed-batch process, Springer-Verlag (2002), whichis hereby incorporated by reference. Examples of minerals includeminerals and mineral salts that can supply nutrients comprising P, K,Mg, S, Ca, Fe, Zn, Mn, and Cu.

Fermentation Products:

A fermentation product can be any substance derived from thefermentation. The fermentation product can be, without limitation, analcohol (e.g., arabinitol, n-butanol, isobutanol, ethanol, glycerol,methanol, ethylene glycol, 1,3-propanediol [propylene glycol],butanediol, glycerin, sorbitol, and xylitol); an alkane (e.g., pentane,hexane, heptane, octane, nonane, decane, undecane, and dodecane), acycloalkane (e.g., cyclopentane, cyclohexane, cycloheptane, andcyclooctane), an alkene (e.g. pentene, hexene, heptene, and octene); anamino acid (e.g., aspartic acid, glutamic acid, glycine, lysine, serine,and threonine); a gas (e.g., methane, hydrogen (H₂), carbon dioxide(CO₂), and carbon monoxide (CO)); isoprene; a ketone (e.g., acetone); anorganic acid (e.g., acetic acid, acetonic acid, adipic acid, ascorbicacid, citric acid, 2,5-diketo-D-gluconic acid, formic acid, fumaricacid, glucaric acid, gluconic acid, glucuronic acid, glutaric acid,3-hydroxypropionic acid, itaconic acid, lactic acid, malic acid, malonicacid, oxalic acid, oxaloacetic acid, propionic acid, succinic acid, andxylonic acid); and polyketide. The fermentation product can also beprotein as a high value product.

In a preferred aspect, the fermentation product is an alcohol. It willbe understood that the term “alcohol” encompasses a substance thatcontains one or more hydroxyl moieties. In a more preferred aspect, thealcohol is n-butanol. In another more preferred aspect, the alcohol isisobutanol. In another more preferred aspect, the alcohol is ethanol. Inanother more preferred aspect, the alcohol is methanol. In another morepreferred aspect, the alcohol is arabinitol. In another more preferredaspect, the alcohol is butanediol. In another more preferred aspect, thealcohol is ethylene glycol. In another more preferred aspect, thealcohol is glycerin. In another more preferred aspect, the alcohol isglycerol. In another more preferred aspect, the alcohol is1,3-propanediol. In another more preferred aspect, the alcohol issorbitol. In another more preferred aspect, the alcohol is xylitol. See,for example, Gong, C. S., Cao, N. J., Du, J., and Tsao, G. T., 1999,Ethanol production from renewable resources, in Advances in BiochemicalEngineering/Biotechnology, Scheper, T., ed., Springer-Verlag BerlinHeidelberg, Germany, 65: 207-241; Silveira, M. M., and Jonas, R., 2002,The biotechnological production of sorbitol, Appl. Microbiol.Biotechnol. 59: 400-408; Nigam, P., and Singh, D., 1995, Processes forfermentative production of xylitol—a sugar substitute, ProcessBiochemistry 30 (2): 117-124; Ezeji, T. C., Qureshi, N. and Blaschek, H.P., 2003, Production of acetone, butanol and ethanol by Clostridiumbeijerinckii BA101 and in situ recovery by gas stripping, World Journalof Microbiology and Biotechnology 19 (6): 595-603.

In another preferred aspect, the fermentation product is an alkane. Thealkane can be an unbranched or a branched alkane. In another morepreferred aspect, the alkane is pentane. In another more preferredaspect, the alkane is hexane. In another more preferred aspect, thealkane is heptane. In another more preferred aspect, the alkane isoctane. In another more preferred aspect, the alkane is nonane. Inanother more preferred aspect, the alkane is decane. In another morepreferred aspect, the alkane is undecane. In another more preferredaspect, the alkane is dodecane.

In another preferred aspect, the fermentation product is a cycloalkane.In another more preferred aspect, the cycloalkane is cyclopentane. Inanother more preferred aspect, the cycloalkane is cyclohexane. Inanother more preferred aspect, the cycloalkane is cycloheptane. Inanother more preferred aspect, the cycloalkane is cyclooctane.

In another preferred aspect, the fermentation product is an alkene. Thealkene can be an unbranched or a branched alkene. In another morepreferred aspect, the alkene is pentene. In another more preferredaspect, the alkene is hexene. In another more preferred aspect, thealkene is heptene. In another more preferred aspect, the alkene isoctene.

In another preferred aspect, the fermentation product is an amino acid.In another more preferred aspect, the organic acid is aspartic acid. Inanother more preferred aspect, the amino acid is glutamic acid. Inanother more preferred aspect, the amino acid is glycine. In anothermore preferred aspect, the amino acid is lysine. In another morepreferred aspect, the amino acid is serine. In another more preferredaspect, the amino acid is threonine. See, for example, Richard, A., andMargaritis, A., 2004, Empirical modeling of batch fermentation kineticsfor poly(glutamic acid) production and other microbial biopolymers,Biotechnology and Bioengineering 87 (4): 501-515.

In another preferred aspect, the fermentation product is a gas. Inanother more preferred aspect, the gas is methane. In another morepreferred aspect, the gas is H₂. In another more preferred aspect, thegas is CO₂. In another more preferred aspect, the gas is CO. See, forexample, Kataoka, N., A. Miya, and K. Kiriyama, 1997, Studies onhydrogen production by continuous culture system of hydrogen-producinganaerobic bacteria, Water Science and Technology 36 (6-7): 41-47; andGunaseelan V. N. in Biomass and Bioenergy, Vol. 13 (1-2), pp. 83-114,1997, Anaerobic digestion of biomass for methane production: A review.

In another preferred aspect, the fermentation product is isoprene.

In another preferred aspect, the fermentation product is a ketone. Itwill be understood that the term “ketone” encompasses a substance thatcontains one or more ketone moieties. In another more preferred aspect,the ketone is acetone. See, for example, Qureshi and Blaschek, 2003,supra.

In another preferred aspect, the fermentation product is an organicacid. In another more preferred aspect, the organic acid is acetic acid.In another more preferred aspect, the organic acid is acetonic acid. Inanother more preferred aspect, the organic acid is adipic acid. Inanother more preferred aspect, the organic acid is ascorbic acid. Inanother more preferred aspect, the organic acid is citric acid. Inanother more preferred aspect, the organic acid is 2,5-diketo-D-gluconicacid. In another more preferred aspect, the organic acid is formic acid.In another more preferred aspect, the organic acid is fumaric acid. Inanother more preferred aspect, the organic acid is glucaric acid. Inanother more preferred aspect, the organic acid is gluconic acid. Inanother more preferred aspect, the organic acid is glucuronic acid. Inanother more preferred aspect, the organic acid is glutaric acid. Inanother preferred aspect, the organic acid is 3-hydroxypropionic acid.In another more preferred aspect, the organic acid is itaconic acid. Inanother more preferred aspect, the organic acid is lactic acid. Inanother more preferred aspect, the organic acid is malic acid. Inanother more preferred aspect, the organic acid is malonic acid. Inanother more preferred aspect, the organic acid is oxalic acid. Inanother more preferred aspect, the organic acid is propionic acid. Inanother more preferred aspect, the organic acid is succinic acid. Inanother more preferred aspect, the organic acid is xylonic acid. See,for example, Chen, R., and Lee, Y. Y., 1997, Membrane-mediatedextractive fermentation for lactic acid production from cellulosicbiomass, Appl. Biochem. Biotechnol. 63-65: 435-448.

In another preferred aspect, the fermentation product is polyketide.

Recovery.

The fermentation product(s) can be optionally recovered from thefermentation medium using any method known in the art including, but notlimited to, chromatography, electrophoretic procedures, differentialsolubility, distillation, or extraction. For example, alcohol isseparated from the fermented cellulosic or xylan-containing material andpurified by conventional methods of distillation. Ethanol with a purityof up to about 96 vol. % can be obtained, which can be used as, forexample, fuel ethanol, drinking ethanol, i.e., potable neutral spirits,or industrial ethanol.

The present invention is further described by the following examplesthat should not be construed as limiting the scope of the invention.

EXAMPLES Example 1

Computer algorithm for classifying related biopolymers in groups andfinding n-mer sequences with a predefined frequency and example ofclassifying animal proteins with related function and sequence in sixseparate groups.

Algorithm

The algorithm to be implemented was:

-   -   1. For each biopolymer make all the n-mers that occur in the        biopolymer sequence.    -   2. Select all biopolymer that contain more than a defined number        of the n-mers.    -   3. Make all the n-mers that occur in these biopolymers and a        defined number of the most abundant n-mers.    -   4. Go back to step 2 until no new n-mers are made in the        following round.        Program

The computer program is written in the Ruby programming language version1.8.6 and normally executed on a machine with the Microsoft Windows XPversion 2002 operative system but can also be executed under otheroperative systems and would easily be adapted to other versions of Ruby.The computer program is disclosed in the Computer Program ListingAppendix.

The input consists of a text file (“.txt” in windows format) containingbiopolymer sequences in FASTA format. In the present example the inputfile is called “six_families.txt” and contains 105 different proteinsequences.

“classify_family3.rb” can be opened in a text editor such as notepad,SciTE, wordpad, MSword or other to define a number of parameters. Themost frequently used parameters are:

cut_off: The number of selected n-mers that are present in a biopolymershould be larger than this value to include the biopolymer in the groupthat is defined by the n-mers.

limit: Number of n-mers that are selected based on frequency. E.g.;limit=100 means that the 100 most frequently occurring n-mers will beselected.

pep_length: Length of the n-mers.

The value of these three parameters is listed in lines 1-3 of“classify_family3.rb”. Other parameters may be changed, e.g., file namesor information written to the log file may be changed.

In the present example the parameters are: cut_off=9 (A protein shouldcontain at least 10 of the selected peptides to be included in thegroup); limit=100 (The 100 most frequently occurring peptides areselected); and pep_length=6 (The peptides are hexamers (six amino acidslong)).

Classes, arrays, methods and other parameters and objects may be namedas “amino acid”, “peptide”, “protein” or similar referring to peptideand amino acid nomenclature but the program works just as well forbiopolymers and n-mers consisting of nucleotide sequences.

When executing “classify_family3.rb” the algorithm will generate twooutput files for each group of biopolymers:

One file (“group_n.txt” where n is an integer) with the selectedbiopolymers in FASTA format and with the score included in the name lineof the sequence (The score is the number of selected n-mers that werefound in the protein).

Another file (“group_n_peps.txt” where n is the same integer) with thecorresponding selected n-mer sequences listed according to frequence ofoccurrence (frequency). In addition, the following information abouteach n-mer is listed:

Position: The median position in the selected biopolymers that containthe n-mer.

Hits: Number of biopolymers in the group that contain the n-mer. This isthe same as frequency.

Degeneracy: Number of nucleotide sequences that will encode the n-mer,last nucleotide not included if this position is degenerate,

Degeneracy_w_l: Same as degeneracy but with nucleotide positions thatcan include all four bases (A, C, G, T) substituted with an inosine thatis not degenerate.

Degeneracy and degeneracy_w_l are only relevant when the n-mers arepeptides. “group_n_peps.txt” is a text file that can be opened as suchor opened or imported into MS excel Open Office calc or another spreadsheet.

In addition to the files for each group, the program will write selectedinformation about the result to a logfile called“parameter_variation.txt”.

In the present example, the information written to the logfile is thedate of the run, number of input sequences, values for limit, cut_offand pep_length, number of groups generated, and for each group: Groupnumber, activity of the protein used to generate the first set ofhexapeptides for generation of the group and number of proteins includedin the group.

Protein Sequences:

The proteins included in the input file (accession numbers: 1705782,224983391, 224983654, 301757408, 301785071, 296474442, 77736363,114053227, 115496822, 260789607, 296211128, 296198149, 73997778,54114982, 145558686, 148231179, 18858509, 113682259, 19880484,194211581, 198443141, 2506136, 1345958, 193695213, 157115283, 301754163,312376091, 158299938, 66515350, 60592790, 170587440, 309360367,268566311, 212642053, 308499509, 73964695, 148841334, 78214939,170038418, 292619618, 229366888, 225718944, 41152191, 225716152,57525242, 159159985, 3043445, 225713940, 126302643, 225705832,149546904, 225706882, 114627636, 226372738, 157817161, 209737752,148228671, 296487921, 45709387, 45382955, 38512205, 62088936, 291389251,114644522, 149031929, 5069468, 38511776, 148232916, 260831456,296215214, 73963109, 292619987, 176866349, 317419553, 4885563, 28557781,241293326, 22085162, 114653371, 291239731, 47224750, 270010958,301757916, 209447036, 296203637, 73993349, 73993361, 57104988,149730179, 224458362, 35920, 4507047, 189053509, 109120366, 4096268,148673899, 291410388, 114649243, 114649241, 114649245, 55730091,297693777, 18181964, 6981556 and 60302866) were found in databasesprovided by the National Center for Biotechnology Information bysearching for proteins related to the following protein names: “fattyacid synthetases”, “cyclin D”, “EDF-1”, “SP1”, “PKC” and “cationic aminoacid transporter 1” and sequences related to these names.

Each protein was assigned a number between “>” and “gi” in the name lineof the FASTA formatted sequence. The number can be used for manualtracking of the origin of the protein:

-   -   Numbers below 100: fatty acid synthetases (FAS)    -   Numbers between 100 and 200: cyclin D (cycD)    -   Numbers between 200 and 300: Endothelial Differentiation Factor        1 (EDF-1)    -   Numbers between 300 and 400: Sp1 transcription factor (SP1)    -   Numbers between 400 and 500: Protein Kinase C (PKC)    -   Numbers between 500 and 600: Cationic Amino Acid Transporter 1        (CAT1)        Results

The input file contained animal protein sequences of six differenttypes. Between 11 and 23 proteins sequence of each type were included.

Execution of “classify_family3.rb” classified the proteins into sixgroups with the corresponding files: “group_ttxt”, “group_1_peps.txt”,“group_2.txt”, “group_2_peps.txt”, “group_3.txt”, “group_3_peps.txt”,“group_4.txt”, “group_4_peps.txt”, “group_5.txt”, “group_5_peps.txt”,“group_6.txt”, “group_6_peps.txt”.

The groups and the sequences were related in the following ways as shownbelow in

TABLE 1 Group number Proteins Protein accession numbers 1 All (23) CAT1-301757916, 209447036, 296203637, type proteins 73993349, 73993361,57104988, 149730179, 224458362, 35920, 4507047, 189053509, 109120366,4096268, 148673899, 291410388, 114649243, 114649241, 114649245,55730091, 297693777, 18181964, 6981556, 60302866 2 All (20) FAS-198443141, 2506136, 1345958, type proteins 193695213, 157115283,301754163, 312376091, 158299938, 66515350, 60592790, 170587440,309360367, 268566311, 212642053, 308499509, 73964695, 148841334,78214939, 170038418, 292619618 3 All (20) cycD- 1705782, 224983391,224983654, type proteins 301757408, 301785071, 296474442, 77736363,114053227, 115496822, 260789607, 296211128, 296198149, 73997778,54114982, 145558686, 148231179, 18858509, 113682259, 19880484, 1942115814 All (17) EDF1- 229366888, 225718944, 41152191, type proteins225716152, 57525242, 159159985, 3043445, 225713940, 126302643,225705832, 149546904, 225706882, 114627636, 226372738, 157817161,209737752, 148228671 5 All (14) PKC- 260831456, 296215214, 73963109,type proteins 292619987, 176866349, 317419553, 4885563, 28557781,241293326, 22085162, 114653371, 291239731, 47224750, 270010958 6 All(11) SP1- 296487921, 45709387, 45382955, type proteins 38512205,62088936, 291389251, 114644522, 149031929, 5069468, 38511776, 148232916Conclusion

As seen from Table 1, all sequences were classified together with theother proteins of the same type as expected. This result shows that thealgorithm executed by “classify_family3.rb” is able to classify manysequences of several different types into functionally related groups.Furthermore, the program provides a library of the most frequentlyoccurring hexapeptides for each group. This library is useful forfurther characterization of the protein, for generation of degeneratedprimers or probes or other purposes related to understanding the proteingroups.

Example 2

Classification of GH61 Proteins in New Groups.

Input Sequences:

Names and sequences of 467 proteins with a glycosyl-hydrolase family 61domain accession numbers:

74667001, 74623591, 296439555, 262118542, 296439558, 74681380, 166327,225557038, 150407066, 239612339, 239607981, 261199970, 261202604,291178704, 296817237, 119403851, 119403039, 119402879, 121706932,121699858, 121701491, 119401707, 238490450, 220691752, 238497908,238491658, 238503077, 220700751, 159129837, 159122044, 159123538,66848476, 70986426, 70994524, 66853425, 70986442, 42820662, 259486007,67517718, 259480946, 40740355, 40739935, 259479347, 259480639,259487791, 75859132, 40739882, 259481977, 134082518, 134080048,145239987, 145258912, 145246562, 145249108, 169772537, 169776393,169772353, 83766624, 83770187, 83775441, 83774271, 114192450, 114196513,114192138, 114196092, 114189374, 115385899, 115391767, 115401906,115433194, 114192785, 115491813, 115401646, 194010899, 157679842,154319179, 150848256, 150843601, 154291544, 154305677, 154305687,150846167, 150843791, 154303615, 154321720, 116198863, 116197146,88180011, 116208464, 116196852, 88179151, 116194372, 88176999, 88175803,88177898, 116206022, 116208766, 88180297, 116201473, 88184980,116178904, 88176171, 116193969, 116208324, 88178730, 88178174, 88178872,116181126, 88182035, 116208244, 88181972, 88184289, 88179554, 88182057,116195750, 88181172, 116202763, 116199761, 116203843, 116179468,88178947, 116199201, 88184520, 88177588, 116196738, 116200237,116199041, 116200816, 116203395, 119183059, 240109478, 23429037,116503205, 116498049, 116497843, 299742296, 299741430, 116506365,299744767, 169851646, 299741891, 299742644, 299753892, 169856301,116506859, 298405205, 299747134, 116500962, 298409438, 169855583,298408738, 298405278, 169863978, 298404712, 298405412, 169857546,298408101, 116497409, 298405114, 298408187, 169868872, 169866035,116504243, 298405932, 169856214, 299754619, 298405923, 134107111,57223077, 46118057, 46115580, 46119467, 46139947, 46110641, 46115706,46116252, 46124039, 46127069, 46127267, 46123465, 46123419, 46123661,209570280, 209570302, 209570284, 209570424, 31747162, 2315274,170102152, 170092074, 164651300, 164636998, 164642401, 170109392,164642863, 164642075, 170105517, 170101484, 170105309, 145011373,145011030, 145020107, 145014411, 145011646, 145015510, 145019304,145016906, 145017744, 145014077, 145015931, 145021993, 39945800,39968819, 145603548, 39946206, 149209397, 145608220, 145608962,39972659, 145607904, 39971969, 39944092, 145605188, 145609409,238616327, 238615335, 215456441, 238568683, 238587009, 238583365,238591056, 215461462, 238579289, 238590448, 215458915, 215450835,215451124, 238587956, 238567983, 238569868, 238579260, 215458309,238616405, 302911456, 302883424, 302911391, 302888437, 302885549,256726867, 302890355, 302885390, 302889367, 302887358, 256726596,256727058, 256726169, 119498947, 119406222, 119485741, 119500958,119415683, 119481757, 119495445, 119474543, 119481769, 28919725,28920895, 85118747, 85078092, 28919956, 28924255, 28919596, 28925415,28920933, 157071792, 85119231, 85107660, 28881165, 18376179, 16945376,211583790, 255933578, 255945663, 255937397, 212532291, 111056092,160705691, 160701235, 169617890, 111070506, 160706762, 111061286,169596753, 160703463, 169596264, 111068298, 160705400, 169616886,111060360, 160706840, 111065694, 169598246, 169622513, 169598063,169594960, 169604850, 169608836, 111069743, 160704974, 160701263,169617193, 111062780, 169619068, 160703254, 21694047, 170936818,171693009, 171677338, 170939885, 171685476, 170946510, 171679531,171676648, 170946519, 171680024, 170941538, 170936992, 170942657,171683179, 171683736, 170945726, 170944138, 171684255, 170941524,170941094, 170945939, 171694598, 171681337, 171688168, 171692645,171690944, 171681359, 171683760, 170942722, 171681569, 170942522,170941813, 170939504, 242218042, 242217378, 220731934, 220723726,189198079, 187980642, 189199012, 189194773, 189193113, 187983705,187976621, 187983395, 189201760, 189207084, 189188194, 189200058,187979887, 189188372, 187977147, 187984916, 189200631, 189192108,189193871, 189205641, 187972977, 187983372, 189191958, 187979866,189194025, 302686954, 300103229, 300103287, 300108602, 300101553,300111682, 302696233, 300105858, 302674513, 300100257, 300103639,300106070, 302675767, 300101263, 302683644, 302679828, 302682756,300101194, 300103387, 302677564, 300100552, 300100648, 302689207,300105576, 302674561, 300101299, 154700549, 156063440, 154694216,156050139, 156045950, 154700442, 156039846, 154700551, 156049573,289621959, 289615175, 289616424, 289621869, 289618672, 289622259,289614784, 289619034, 289615496, 289618626, 289616197, 289616196,289617770, 289620809, 289620945, 289620832, 289621556, 289615045,289618715, 289618337, 148553353, 218722209, 284451272, 201066457,299892806, 302656446, 296418037, 295636680, 237904675, 302409770,261358989, 302420443, 261361024, 302410193, 261352381, 261358929,302414852, 302418676, 261360020, 302413657, 302417124, 302405483,261353895, 302419149, 261358115, 302405803, 261359888, 261359952,302405821, 261361512, 302409258, 49333361, 238011426, 194704134, and11359621 were used as input.

Algorithm and Implementation

The same program as in example 1 was used with the parameters cut_off=9,limit=100 and pep_length=6.

Results

The program was executed with the 467 gh61 proteins as input. After 13rounds the groups became too small (five or less proteins) to define anycommon peptide profile because the remaining proteins had very differentsequences. However, 13 round defined the groups as listed in Table 2.Each group had its own profile of hexapeptides (100 most frequentlyoccurring hexapeptides) with little overlap between groups asillustrated in Table 3.

TABLE 2 Groups of GH61 proteins Group Proteins 1 86 2 43 3 27 4 24 5 196 18 7 15 8 15 9 14 10 14 11 13 12 10 13 9

TABLE 3 Cross comparison of the hexapeptide signatures for each group(group) of GH61 proteins Subfamily 1 2 3 4 5 6 7 8 9 10 11 12 13 1 100 33 1 0 0 0 5 1 2 3 0 2 2 3 100 12 0 0 1 1 7 0 5 2 1 4 3 3 12 100 7 0 2 04 2 5 3 0 3 4 1 0 7 100 0 1 0 0 2 1 0 1 1 5 0 0 0 0 100 0 0 0 0 0 0 0 06 0 1 2 1 0 100 0 1 6 2 0 0 1 7 0 1 0 0 0 0 100 0 0 0 3 1 0 8 5 7 4 0 01 0 100 0 3 6 1 2 9 1 0 2 2 0 6 0 0 100 0 0 0 0 10 2 5 5 1 0 2 0 3 0 1002 0 1 11 3 2 3 0 0 0 3 6 0 2 100 0 1 12 0 1 0 1 0 0 1 1 0 0 0 100 0 13 24 3 1 0 1 0 2 0 1 1 0 100Conclusion

The distribution of the hexapeptides showed that almost all theconserved peptides were found in the first 240 amino acids of the gh61proteins whereas the remaining part of the proteins was highly variable.Interestingly, two peaks were observed where most of the conservedhexapeptides were found for all the family. Region 1 located betweenamino acid residues 100-120 has a clear peak whereas region 2 (aminoacids 160-200) has a shoulder at amino acids 200-240. The distributionof peptides for each group shows that groups 1, 5, 7, 8 9, 10 and 12(type 1) only have peaks in regions 1 and 2 whereas groups 2, 3, 4, 6,11 and 13 (type 2) have an additional peak from amino acids 200-220.Peak 1 was very small in group 7, indicating that this group is poorlyconserved in region 1.

To investigate the three conserved regions in more detail we aligned thehexapeptides for each group in these regions to generate a consensussequence. Alignment of the consensus sequences for each group shows thatregion 1 is similar in 11 of the 13 groups and contains one of thehistidines that coordinates the divalent nickel atom bound to the gh61crystal structure (Karkehabadi, S. et al., 2008. The first structure ofa glycoside hydrolase family 61 member, Cel61B from Hypocrea jecorina,at 1.6 A resolution. Journal of Molecular Biology, 383(1), 144-154).Furthermore, the two cysteines that form a cysteine bridge in thecrystal structure were found in this region but were only conserved ingroups 1, 8 and 11. In group 11, the second of the two cysteines wasfound in the protein sequences but was located outside the conservedhexapeptides.

Region 2 was conserved in all 13 groups and contains a conservedhistidine that does not participate in coordination of the nickel atom(Karkehabadi, S. et al., 2008. The first structure of a glycosidehydrolase family 61 member, Cel61B from Hypocrea jecorina, at 1.6 Aresolution. Journal of Molecular Biology, 383(1), 144-154) butnevertheless is located on the nickel-binding surface of gh61 togetherwith two other conserved residues (Q/E49 and Y51) in region 2. Region 3is outside the reported crystal structure and contains a conservedproline-glycine dipeptide.

To further compare the groups we aligned the proteins that gave thehighest score in each group. Notably, this alignment showed that His23that participates in binding to the nickel atom was conserved in allfamilies. Also the two cysteines (Cys78 and Cys228) that form a cysteinebridge in the crystal were conserved. Interestingly, the alignment ispoor between amino acids 60 and 80 where several residues map to thenickel binding surface of gh61. Thus the herein described algorithmprogrammed as in example 1 is able to divide a large number of highlydivergent gh61 family proteins into comprehensible groups.

Example 3

Generation of primers to isolate novel genes belonging to GH61 group 1genes.

Design of Degenerated Primers

Conserved hexapeptides identified in example 2 were reverse translatedaccording to the genetic code and positions containing any nucleotide(A, C, G or T) were substituted with inosine (Table 4). Degeneratenucleotides at the 3′ end of the primers were removed from the sequenceof the primers. The degeneracy of the primer that results from reversetranslation of each hexapeptide was calculated based on the genetic codeand substituting positions containing any nucleotide (A, C, G or T) withinosine (Table 4). In addition, the relative position of thehexapeptides in the proteins was estimated as the median of the distanceof the peptide to the N-terminal of each protein in the subgroup thatcontained the peptide.

Sequences for primers were selected on three criteria:

-   -   1. They should have high frequency in the subfamily of proteins    -   2. They should give an amplicon of at least 40 base pairs        excluding primer sequences in order to be able to get sufficient        sequence information to identify the PCR product.    -   3. The primers should have the smallest possible redundancy and        redundant bases at the 3′ end are not allowed.

A tail of six bases (CTGGAC) was added to the 5′ end of all primersequences as this is reported to improve the performance of shortprimers. Reverse primers were designed to be reverse complementary tothe DNA sequence encoding the hexapeptide and according to the samerules. The primers were synthesized and HPLC-purified by Sigma-Aldrich(UK/Europe).

TABLE 4 List of degenerated primers Primer Peptide nameFinal primer sequence DIICHK (SEQ ID NO: 104) 61.1CTGGACGAYATHATHTGYCAYAA (SEQ ID NO: 80) EIIALH (SEQ ID NO: 105) 61.2CTGGACTGIAGIGCDATDATYTC (SEQ ID NO: 81 HHGPV (SEQ ID NO: 106) 61.3CTGGACCAYCAYGGICCIGT (SEQ ID NO: 82) GAQNYP (SEQ ID NO: 107) 61.4CTGGACGGRTARTTYTGIGCICC (SEQ ID NO: 83) LEFFKI (SEQ ID NO: 108) 61.5CTGGACCTIGARTTYTTYAARAT (SEQ ID NO: 84)Fungi

The following fungi as listed in table 6 were purchased from TheCentraalbureau voor Schimmelcultures, The Netherlands and grown on 6%wheat bran (Finax, Denmark), 15% agar (Sigma-Aldrich, UK/Europe) platesat the recommended temperature.

TABLE 5 List of fungi Fungus CBS number Chaetomium senegalense 728.84Chaetomium thermophilum 180.67 Corynascus thermophilus 406.69Malbranchea cinnamomea 115.68 Melanocarpus albomyces 638.94 Remersoniathermophila 540.69 Scytalidium indonesiacum 259.81 Scytalidiumthermophilum 620.91 Talaromyces byssochlamydoides 151.75 Talaromycesemersonii 393.64 Talaromyces leycettanus 398.68 Talaromyces thermophilus236.58 Thermoascus aurantiacus 891.70 Thermomyces lanuginosus 632.91DNA Purification

Fungal mycelium was scraped of the top of a wheat bran agar plate,frozen in N₂(I) and grinded with a mortar and pestle. DNA was extractedfrom the homogenized mycelium with the Fungal DNA Mini Kit (OmegaBio-Tek, USA) according to the manufacturer's instructions.

PCR

A mix of 100 ng total fungal RNA in 1× Run PCR buffer, 2 mM each dATP,dCTP, dGTP and dTTP, 400 nM forward primer; 400 nM reverse primer; 1URUN DNA polymerase (A&A Biotechnology, Poland) in a total volume of 20μl was used for PCR on an MyCycler (Bio-Rad, USA) with the followingthermal profile: Initial denaturation 95° C., 5 minutes. 40 cycles of95° C., 20 seconds; 54° C., 30 seconds; 72° C., 60 seconds and a finalextension at 72° C. 5 minutes. PCR products were analyzed by agarose gelelectrophoresis and selected DNA were cut out and purified using aQIAQUICK® Kit (QIAGEN, Germany). One μl of the purified PCR product wasreamplified in a 50 μl reaction under the same conditions as theoriginal PCR except that only 15 to 20 cycles of PCR were performed.

Sequencing and Analysis

PCR products were cycle sequenced by Eurofins-MWG (Germany) or StarSEQ(Germany) with one of the degenerated primers used for PCR. Theresulting sequences were translated to amino acid sequence and used forBLAST search (Altschul et al., 1997) against the non-redundant proteinsequence database at NCBI and inspected for conserved domains(Marchler-Bauer et al., 2009) in the CDD database at NCBI to identifysequences encoding glycoside hydrolase family 61-like proteins.

Results

The most frequently occurring hexapeptides defining group 1 of GH61swere used for design of degenerated primers (Table 4). As the two mostconserved hexapeptides (occurring in 80 and 78% of the proteins) couldbe used for design of reverse primers we did not find it necessary todesign a third reverse primer. One of the three hexapeptides used forforward primer design (SHHGPV) contains one serine residue that is codedby 6 different codons at the N-terminal. A degenerate primer to serinedoes not contribute significantly to specificity and therefore, theprimer was made by reverse translation of the peptide HHGPV. In virtualPCR the three forward and two reverse primers were able to amplify 66 ofthe 85 proteins in group 1 and no proteins from other groups.

The primers were used for all six possible combinations for PCR of DNAfrom the 14 thermophilic fungi.

For all the fungi at least one of the primer sets gave an amplificationproduct with the expected size and for some fungi all the primer setsgave a positive product. For each fungus, the longest ampliqon that hadthe expected size was sequenced and analyzed for open reading frames.All the ampliqons yielded a sequence that encodes a novel, putative GH61family gene. Although the isolated sequences are only partial, it waspossible to classify all except one as belonging to group 1. Theunassigned sequence from Chaetomium senegalense was the shortest of thesequences and is only 37 amino acids long but had up to 73% identity toknown gh61 sequences and 78% identity to the new sequence fromRemersonia thermophila. In fact, it is surprising that the some of thenew sequences had so many of the conserved hexapeptides. E.g.; thepartial gh61 sequence from Maibranchea cinnamomea had 17 of theconserved peptides from group 1 although the sequence is only 73 aminoacids long. In summary, the PCR result showed that degenerated primersbased on the hexapeptide finder algorithm could be used to find new gh61proteins.

Example 4

Generation of primers to isolate novel genes belonging to GH6, GH7 andGH45 genes.

Using the same approach conserved hexapeptides was identified for theGH6, 7 and 45 families.

Input Sequences:

Names and sequences of: 17 proteins with a glycosyl-hydrolase family 6domain accession numbers: (119473935, 119495997, 220693815, 70986018,145239297, 145246118, 115401052, 115491303, 67521632, 67538224,95025919, 913560, 60729586, 68270848, 50837707, 50837690, 50837696)

19 proteins with a glycosyl-hydrolase family 7 domain accession numbers:(950686, 4883502, 156712278, 156712280, 156712284, 20986705, 27125837,150021831, 29160357, 117935080, 58045187, 156712282, 50844407, 2761,950686, 950688, 4883502, 7224903, 29160311)

12 proteins with a glycosyl-hydrolase family 45 domain accessionnumbers: (154294519, 222103630, 116180480, 310789959, 312217600,39951371, 169616266, 171687659, 189197649, 27530617, 156032908 and158138919) were used as input.

Conserved hexapeptides were identified for the 3 gene families as inExample 2 and the below listed degenerate primes were generated and PCRamplification was performed as described in Example 3.

TABLE 6 List of degenerate primes Target Target Target genes sequenceprimer sequence genes redundancy name GH6 LPDRDC (SEQ IDcaggtccticcigaymgigaytg GH6  512 CBHII.7 NO: 109) (SEQ ID NO: 128) GH6GWLGWP (SEQ ID caggtcggitggctiggitggc (SEQ GH6   64 CBHII.9 NO: 110)ID NO: 129) GH6 GLATNV (SEQ ID caggtcggictigciaciaaygt (SEQ GH6  512CBHII.11 NO: 111) ID NO: 130) GH6 PAPEAG (SEQ IDcaggtcccigcytciggigcigg (SEQ GH6  512 CBHII.6 NO: 112) ID NO: 131) GH6WFQAYF (SEQ ID caggtcaartaigcytgraacca GH6   32 CBHII.8 NO: 113)(SEQ ID NO: 132) GH6 VVYDLP (SEQ ID ctggacgtigtitaygaycticc (SEQ GH6 256 cbhII.13 NO: 114) ID NO: 133) GH6 WVKPGG (SEQ IDctggacccicciggyttiaccca SEQ GH6  128 cbhII.10 NO: 115) ID NO: 134) GH7DANWRN (SEQ ID ctggacgaygciaaytggmgitgg GH7  128 cbhI.1 NO: 116)(SEQ ID NO: 135) GH7 EFTFDVD (SEQ ID ctggacgarttyacittygaygtiga GH7  256cbhI.3 NO: 117) (SEQ ID NO: 136) GH7 GTGYCD (SEQ IDctggacggiaciggitaytgyga GH7  256 cbhI.5 NO: 118) (SEQ ID NO: 137) GH7EMDIWEA (SEQ ID ctggacgcytcccadatrtccatytc GH7   24 cbhI.2 NO: 119)(SEQ ID NO: 138) GH7 DGCDFN (SEQ ID ctggacttraartcrcaiccrtc GH7   64cbhI.4 NO: 120) (SEQ ID NO: 139) GH7 VVTQF (SEQ IDctggacaaytgigtiaciac (SEQ GH7  128 cbhI.6 NO: 121) ID NO: 140) GH45YWDCCK (SEQ ID caggtctaytgggaytgytgyaa GH45   16 GH45.3 NO: 122)(SEQ ID NO: 141) GH45 PGGGVG (SEQ ID caggtccciaciccicciccigg (SEQ GH451024 GH45.6 NO: 123) ID NO: 142) GH45 WR(F/Y)(D/N)WFcaggtcaaccarttrtaickcaa (SEQ GH45  128 GH45.8 (SEQ ID NO: 124)ID NO: 143) GH45 WCCACY (SEQ ID ctggactggtgytgygcitgyta (SEQ GH45   3245.5 NO: 125) ID NO: 144) GH45 WCCACY (SEQ ID ctggactarcaigcrcarcaccaGH45   32 45.10 NO. 126) (SEQ ID NO. 145) GH45 WDCCKP (SEQ IDctggactgggaytgytgyaarcc GH45   16 45.7 NO: 127) (SEQ ID NO: 146)Results

By performing PCR amplification of DNA isolated from the 14 fungi listedin Table 5 using combinations of the degenerate primes listed in table 6and sequence analysis of the resulting amplified DNA fragments lead tothe isolation of fragments of 6 novel GH6 genes, 8 novel GH7 genes and10 novel GH45 genes.

The present invention is further described by the following numberedparagraphs:

[1] An isolated polypeptide having cellobiohydrolase activity, selectedfrom the group consisting of: (a) a polypeptide having at least 80%sequence identity to the polypeptide of SEQ ID NO: 2 or SEQ ID NO: 4; atleast 90% sequence identity to the polypeptide of SEQ ID NO: 6; at least91% sequence identity to the polypeptide of SEQ ID NO: 8; or at least99% sequence identity to the polypeptide of SEQ ID NO: 10; (b) apolypeptide encoded by a polynucleotide that hybridizes under at leastvery high stringency conditions with (i) the polypeptide coding sequenceof SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, or SEQ ID NO:9, (ii) the cDNA sequence thereof, or (iii) the full-length complementof (i) or (ii); (c) a polypeptide encoded by a polynucleotide having atleast 80% sequence identity to the polypeptide coding sequence of SEQ IDNO: 1 or SEQ ID NO: 3, or the cDNA sequences thereof; at least 90%sequence identity to the polypeptide coding sequence of SEQ ID NO: 5 orthe cDNA sequence thereof; at least 91% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 7 or the cDNA sequencesthereof; or at least 99% sequence identity to the polypeptide codingsequence of SEQ ID NO: 9 or the cDNA sequence thereof; (d) a variantcomprising the polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6,SEQ ID NO: 8, or SEQ ID NO: 10 comprising a substitution, deletion,and/or insertion at one or more (e.g., several) positions; and (e) afragment of the polypeptide of (a), (b), (c), or (d) that hascellobiohydrolase activity.

[2] The polypeptide of paragraph 1, having at least 80%, at least 81%,at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 2 or SEQ ID NO: 4; at least 90%, at least 91%,at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 6; at least 91%, at least 92%, at least 93%,at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 8;or at least 99% or 100% sequence identity to the polypeptide of SEQ IDNO: 10.

[3] The polypeptide of paragraph 1, which is encoded by a polynucleotidethat hybridizes under very high stringency conditions with (i) thepolypeptide coding sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5,SEQ ID NO: 7, or SEQ ID NO: 9, (ii) the cDNA sequence thereof, or (iii)the full-length complement of (i) or (ii).

[4] The polypeptide of paragraph 1, which is encoded by a polynucleotidehaving at least 80%, at least 81%, at least 82%, at least 83%, at least84%, at least 85%, at least 86%, at least 87%, at least 88%, at least89%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 1 or SEQ ID NO: 3, or the cDNA sequences thereof; at least 90%,at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 5 or the cDNAsequence thereof; at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 7 or the cDNA sequences thereof; or at least 99% or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 9 or the cDNAsequence thereof.

[5] The polypeptide of any of paragraphs 1-4, comprising or consistingof SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, or SEQ ID NO:10 or the polypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQID NO: 8, or SEQ ID NO: 10.

[6] The polypeptide of paragraph 1, which is a variant comprising thepolypeptide of SEQ ID NO: 2, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8,or SEQ ID NO: 10 comprising a substitution, deletion, and/or insertionat one or more positions.

[7] The polypeptide of paragraph 1, which is a fragment of SEQ ID NO: 2,SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, or SEQ ID NO: 10, wherein thefragment has cellobiohydrolase activity.

[8] An isolated polypeptide having cellobiohydrolase activity, selectedfrom the group consisting of: (a) a polypeptide having cellobiohydrolaseactivity having at least 70% sequence identity to the polypeptide of SEQID NO: 12; at least 80% sequence identity to the polypeptide of SEQ IDNO: 14 or SEQ ID NO: 16; at least 91% sequence identity to thepolypeptide of SEQ ID NO: 18; at least 96% sequence identity to thepolypeptide of SEQ ID NO: 20; or at least 98% sequence identity to thepolypeptide of SEQ ID NO: 22 or SEQ ID NO: 24; (b) a polypeptide havingcellobiohydrolase activity encoded by a polynucleotide that hybridizesunder at least very high stringency conditions with (i) the polypeptidecoding sequence of SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ IDNO: 17, SEQ ID NO: 19, SEQ ID NO: 21, or SEQ ID NO: 23, (ii) the cDNAsequence thereof, or (iii) the full-length complement of (i) or (ii);(c) a polypeptide having cellobiohydrolase activity encoded by apolynucleotide having at least 70% sequence identity to the polypeptidecoding sequence SEQ ID NO: 11 or the cDNA sequence thereof; at least 80%sequence identity to the polypeptide coding sequence of SEQ ID NO: 13 orSEQ ID NO: 15, or the cDNA sequences thereof; at least 91% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 17 or the cDNAsequence thereof; at least 96% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 19 or the cDNA sequence thereof; or atleast 98% sequence identity to the polypeptide coding sequence of SEQ IDNO: 21 or SEQ ID NO: 23, or the cDNA sequences thereof; (d) acellobiohydrolase variant comprising the polypeptide of SEQ ID NO: 12,SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO:22, or SEQ ID NO: 24 comprising a substitution, deletion, and/orinsertion at one or more positions; and (e) a fragment of thepolypeptide of (a), (b), (c), or (d) that has cellobiohydrolaseactivity.

[9] The polypeptide of paragraph 8, having at least 70%, at least 75%,at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide of SEQ ID NO: 12; at least80%, at least 81%, at least 82%, at least 83%, at least 84%, at least85%, at least 86%, at least 87%, at least 88%, at least 89%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%sequence identity to the polypeptide of SEQ ID NO: 14 or SEQ ID NO: 16;at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide of SEQ ID NO: 18; at least 96%, at least97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 20; or at least 98%, at least 99% or 100%sequence identity to the polypeptide of SEQ ID NO: 22 or SEQ ID NO: 24.

[10] The polypeptide of paragraph 8, which is encoded by apolynucleotide that hybridizes under very high stringency conditionswith (i) the polypeptide coding sequence of SEQ ID NO: 11, SEQ ID NO:13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, or SEQID NO: 23, (ii) the cDNA sequence thereof, or (iii) the full-lengthcomplement of (i) or (ii).

[11] The polypeptide of paragraph 8, which is encoded by apolynucleotide having at least 70%, at least 75%, at least 80%, at least81%, at least 82%, at least 83%, at least 84%, at least 85%, at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityto the polypeptide coding sequence SEQ ID NO: 11 or the cDNA sequencethereof; at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 13 or SEQ ID NO: 15, or the cDNA sequences thereof; atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 17 or the cDNAsequence thereof; at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 19 or the cDNA sequence thereof; or at least 98%, at least 99% or100% sequence identity to the polypeptide coding sequence of SEQ ID NO:21 or SEQ ID NO: 23, or the cDNA sequences thereof.

[12] The polypeptide of any of paragraphs 8-11, comprising or consistingof SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ IDNO: 20, SEQ ID NO: 22, or SEQ ID NO: 24 or the polypeptide of SEQ ID NO:12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ IDNO: 22, or SEQ ID NO: 24.

[13] The polypeptide of paragraph 8, which is a variant comprising thepolypeptide of SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO:18, SEQ ID NO: 20, SEQ ID NO: 22, or SEQ ID NO: 24 comprising asubstitution, deletion, and/or insertion at one or more positions.

[14] The polypeptide of paragraph 8, which is a fragment of SEQ ID NO:12, SEQ ID NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ IDNO: 22, or SEQ ID NO: 242, wherein the fragment has cellobiohydrolaseactivity.

[15] An isolated polypeptide having endoglucanase activity, selectedfrom the group consisting of: (a) a polypeptide having at least 60%sequence identity to the polypeptide of SEQ ID NO: 26; at least 65%sequence identity to the polypeptide of SEQ ID NO: 28; at least 70%sequence identity to the polypeptide of SEQ ID NO: 30 or SEQ ID NO: 32;at least 80% sequence identity to the polypeptide of SEQ ID NO: 34, SEQID NO: 36, or SEQ ID NO: 38; at least 85% sequence identity to thepolypeptide of SEQ ID NO: 40 or SEQ ID NO: 42; at least 97% sequenceidentity to the polypeptide of SEQ ID NO: 44; or at least 98% sequenceidentity to the polypeptide of SEQ ID NO: 46; (b) a polypeptide encodedby a polynucleotide that hybridizes under at least high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 25 orSEQ ID NO: 27, (ii) the cDNA sequence thereof, or (iii) the full-lengthcomplement of (i) or (ii); or under at least very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 29,SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO:39, SEQ ID NO: 41, SEQ ID NO: 43, or SEQ ID NO: 45, (ii) the cDNAsequence thereof, or (iii) the full-length complement of (i) or (ii);(c) a polypeptide encoded by a polynucleotide having at least 60%sequence identity to the polypeptide coding sequence of SEQ ID NO: 25 orthe cDNA sequence thereof; at least 65% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 27 or the cDNA sequencethereof; at least 70% sequence identity to the polypeptide codingsequence of SEQ ID NO: 29 or SEQ ID NO: 31, or the cDNA sequencesthereof; at least 80% sequence identity to the polypeptide codingsequence of SEQ ID NO: 33, SEQ ID NO: 35, or SEQ ID NO: 37, or the cDNAsequences thereof; at least 85% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 39 or SEQ ID NO: 41, or the cDNA sequencesthereof; at least 97% sequence identity to the polypeptide codingsequence of SEQ ID NO: 43 or the cDNA sequence thereof; or at least 98%sequence identity to the polypeptide coding sequence of SEQ ID NO: 45 orthe cDNA sequence thereof; (d) a variant comprising the polypeptide ofSEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO:34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ IDNO: 44, or SEQ ID NO: 46 comprising a substitution, deletion, and/orinsertion at one or more positions; and (e) a fragment of thepolypeptide of (a), (b), (c), or (d) that has endoglucanase activity.

[16] The polypeptide of paragraph 15, having at least 60%, at least 65%,at least 70%, at least 75%, at least 80%, at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 26; at least 65%, e.g., at least 70%, at least 75%, at least80%, at least 81%, at least 82%, at least 83%, at least 84%, at least85%, at least 86%, at least 87%, at least 88%, at least 89%, at least90%, at least 91%, at least 92%, at least 93%, at least 94%, at least95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%sequence identity to the polypeptide of SEQ ID NO: 28; at least 70%, atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 30or SEQ ID NO: 32; at least 80%, at least 81%, at least 82%, at least83%, at least 84%, at least 85%, at least 86%, at least 87%, at least88%, at least 89%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% sequence identity to the polypeptide of SEQID NO: 34, SEQ ID NO: 36, or SEQ ID NO: 38; at least 85%, e.g., at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityto the polypeptide of SEQ ID NO: 40 or SEQ ID NO: 42; at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptide ofSEQ ID NO: 44; or at least 98%, at least 99% or 100% sequence identityto the polypeptide of SEQ ID NO: 46.

[17] The polypeptide of paragraph 15, which is encoded by apolynucleotide that hybridizes under high or very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 25 orSEQ ID NO: 27, (ii) the cDNA sequence thereof, or (iii) the full-lengthcomplement of (i) or (ii); or under very high stringency conditions with(i) the polypeptide coding sequence of SEQ ID NO: 29, SEQ ID NO: 31, SEQID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41,SEQ ID NO: 43, or SEQ ID NO: 45, (ii) the cDNA sequence thereof, or(iii) the full-length complement of (i) or (ii).

[18] The polypeptide of paragraph 15, which is encoded by apolynucleotide having at least 60%, at least 65%, at least 70%, at least75%, at least 80%, at least 81%, at least 82%, at least 83%, at least84%, at least 85%, at least 86%, at least 87%, at least 88%, at least89%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 25 or the cDNA sequence thereof; at least 65%, at least 70%, atleast 75%, at least 80%, at least 81%, at least 82%, at least 83%, atleast 84%, at least 85%, at least 86%, at least 87%, at least 88%, atleast 89%, at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 27 or the cDNA sequence thereof; at least 70%, at least75%, at least 80%, at least 81%, at least 82%, at least 83%, at least84%, at least 85%, at least 86%, at least 87%, at least 88%, at least89%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 29 or SEQ ID NO: 31, or the cDNA sequences thereof; at least 80%,at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 33, SEQ ID NO:35, or SEQ ID NO: 37, or the cDNA sequences thereof; at least 85%, atleast 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 39 or SEQ IDNO: 41, or the cDNA sequences thereof; at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide coding sequenceof SEQ ID NO: 43 or the cDNA sequence thereof; or at least 98%, at least99% or 100% sequence identity to the polypeptide coding sequence of SEQID NO: 45 or the cDNA sequence thereof.

[19] The polypeptide of any of paragraphs 15-18, comprising orconsisting of SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO:32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ IDNO: 42, SEQ ID NO: 44, or SEQ ID NO: 46 or the polypeptide of SEQ ID NO:26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ IDNO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, orSEQ ID NO: 46.

[20] The polypeptide of paragraph 15, which is a variant comprising thepolypeptide of SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO:32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ IDNO: 42, SEQ ID NO: 44, or SEQ ID NO: 462 comprising a substitution,deletion, and/or insertion at one or more positions.

[21] The polypeptide of paragraph 15, which is a fragment of SEQ ID NO:26, SEQ ID NO: 28, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 34, SEQ IDNO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 44, orSEQ ID NO: 46, wherein the fragment has endoglucanase activity.

[22] An isolated polypeptide having cellulolytic enhancing activity,selected from the group consisting of: (a) a polypeptide having at least70% sequence identity to the polypeptide of SEQ ID NO: 48; at least 75%sequence identity to the polypeptide of SEQ ID NO: 50, SEQ ID NO: 52,SEQ ID NO: 54, or SEQ ID NO: 79; at least 80% sequence identity to thepolypeptide of SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO:62, or SEQ ID NO: 64; at least 85% sequence identity to the polypeptideof SEQ ID NO: 66; or at least 90% sequence identity to the polypeptideof SEQ ID NO: 68 or SEQ ID NO: 70; (b) a polypeptide encoded by apolynucleotide that hybridizes under at least very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 47,SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO:57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ IDNO: 67, SEQ ID NO: 69, or SEQ ID NO: 71, (ii) the cDNA sequence thereof,or (iii) the full-length complement of (i) or (ii); (c) a polypeptideencoded by a polynucleotide having at least 70% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 47 or the cDNA sequencethereof; at least 75% sequence identity to the polypeptide codingsequence of SEQ ID NO: 49, SEQ ID NO: 51, or SEQ ID NO: 53, or the cDNAsequences thereof; at least 80% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ IDNO: 61, or SEQ ID NO: 63, or the cDNA sequences thereof; at least 85%sequence identity to the polypeptide coding sequence of SEQ ID NO: 65 orthe cDNA sequence thereof; or at least 90% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 67, SEQ ID NO: 69, or SEQ IDNO: 71, or the cDNA sequences thereof; (d) a variant comprising thepolypeptide of SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO:54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ IDNO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, orSEQ ID NO: 79 comprising a substitution, deletion, and/or insertion atone or more positions; and (e) a fragment of the polypeptide of (a),(b), (c), or (d) that has cellulolytic enhancing activity.

[23] The polypeptide of paragraph 22, having at least 70%, at least 75%,at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide of SEQ ID NO: 48; at least75%, at least 80%, at least 81%, at least 82%, at least 83%, at least84%, at least 85%, at least 86%, at least 87%, at least 88%, at least89%, at least 90%, at least 91%, at least 92%, at least 93%, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 50, SEQID NO: 52, SEQ ID NO: 54, or SEQ ID NO: 79; at least 80%, at least 81%,at least 82%, at least 83%, at least 84%, at least 85%, at least 86%, atleast 87%, at least 88%, at least 89%, at least 90%, at least 91%, atleast 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or 100% sequence identity to thepolypeptide of SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO:62, or SEQ ID NO: 64; at least 85%, at least 86%, at least 87%, at least88%, at least 89%, at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% sequence identity to the polypeptide of SEQID NO: 66; or at least 90%, at least 91%, at least 92%, at least 93%, atleast 94%, at least 95%, at least 96%, at least 97%, at least 98%, atleast 99%, or 100% sequence identity to the polypeptide of SEQ ID NO:68, SEQ ID NO: 70, or SEQ ID NO: 72.

[24] The polypeptide of paragraph 22, which is encoded by apolynucleotide that hybridizes under very high stringency conditionswith (i) the polypeptide coding sequence of SEQ ID NO: 47, SEQ ID NO:49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ IDNO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65, SEQ ID NO: 67, SEQID NO: 69, or SEQ ID NO: 71, (ii) the cDNA sequence thereof, or (iii)the full-length complement of (i) or (ii).

[25] The polypeptide of paragraph 22, which is encoded by apolynucleotide having at least 70%, at least 75%, at least 80%, at least81%, at least 82%, at least 83%, at least 84%, at least 85%, at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityto the polypeptide coding sequence of SEQ ID NO: 47 or the cDNA sequencethereof; at least 75%, at least 80%, at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 49, SEQ ID NO: 51, or SEQ ID NO: 53, orthe cDNA sequences thereof; at least 80%, at least 81%, at least 82%, atleast 83%, at least 84%, at least 85%, at least 86%, at least 87%, atleast 88%, at least 89%, at least 90%, at least 91%, at least 92%, atleast 93%, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ IDNO: 61, or SEQ ID NO: 63, or the cDNA sequences thereof; at least 85%,at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, atleast 91%, at least 92%, at least 93%, at least 94%, at least 95%, atleast 96%, at least 97%, at least 98%, at least 99%, or 100% sequenceidentity to the polypeptide coding sequence of SEQ ID NO: 65 or the cDNAsequence thereof; or at least 90%, at least 91%, at least 92%, at least93%, at least 94%, at least 95%, at least 96%, at least 97%, at least98%, at least 99%, or 100% sequence identity to the polypeptide codingsequence of SEQ ID NO: 67, SEQ ID NO: 69, or SEQ ID NO: 71, or the cDNAsequences thereof.

[26] The polypeptide of any of paragraphs 22-25, comprising orconsisting of SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO:54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ IDNO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 70, or SEQ ID NO: 72 orthe polypeptide of SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ IDNO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQID NO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72,or SEQ ID NO: 79. [27] The polypeptide of paragraph 22, which is avariant comprising the polypeptide of SEQ ID NO: 48, SEQ ID NO: 50, SEQID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60,SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 69, SEQ ID NO:70, SEQ ID NO: 72, or SEQ ID NO: 79 comprising a substitution, deletion,and/or insertion at one or more positions.

[28] The polypeptide of paragraph 22, which is a fragment of SEQ ID NO:48, SEQ ID NO: 50, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ IDNO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 79, wherein thefragment has cellulolytic enhancing activity.

[29] An isolated polypeptide having xylanase activity, selected from thegroup consisting of: (a) a polypeptide having at least 70% sequenceidentity to the polypeptide of SEQ ID NO: 74, at least 94% sequenceidentity to the polypeptide of SEQ ID NO: 78, or at least 98% sequenceidentity to the polypeptide of SEQ ID NO: 76; (b) a polypeptide encodedby a polynucleotide that hybridizes under at least very high stringencyconditions with (i) the polypeptide coding sequence of SEQ ID NO: 73,SEQ ID NO: 75, or SEQ ID NO: 77, (ii) the cDNA sequence thereof, or(iii) the full-length complement of (i) or (ii); (c) a polypeptideencoded by a polynucleotide having at least 70% sequence identity to thepolypeptide coding sequence of SEQ ID NO: 73 or the cDNA sequencethereof, at least 94% sequence identity to the polypeptide codingsequence of SEQ ID NO: 77 or the cDNA sequence thereof, or at least 98%sequence identity to the polypeptide coding sequence of SEQ ID NO: 75 orthe cDNA sequence thereof; (d) a variant comprising the polypeptide ofSEQ ID NO: 74, SEQ ID NO: 76, or SEQ ID NO: 78 comprising asubstitution, deletion, and/or insertion at one or more positions; and(e) a fragment of the polypeptide of (a), (b), (c), or (d) that hasxylanase activity.

[30] The polypeptide of paragraph 29, having at least 70%, at least 75%,at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, atleast 85%, at least 86%, at least 87%, at least 88%, at least 89%, atleast 90%, at least 91%, at least 92%, at least 93%, at least 94%, atleast 95%, at least 96%, at least 97%, at least 98%, at least 99%, or100% sequence identity to the polypeptide of SEQ ID NO: 74, at least94%, at least 95%, at least 96%, at least 97%, at least 98%, at least99%, or 100% sequence identity to the polypeptide of SEQ ID NO: 78, orat least 98%, at least 99%, or 100% sequence identity to the polypeptideof SEQ ID NO: 76.

[30] The polypeptide of paragraph 29, which is encoded by apolynucleotide that hybridizes under very high stringency conditionswith (i) the polypeptide coding sequence of SEQ ID NO: 73, SEQ ID NO:75, or SEQ ID NO: 77, (ii) the cDNA sequence thereof, or (iii) thefull-length complement of (i) or (ii).

[32] The polypeptide of paragraph 29, which is encoded by apolynucleotide having at least 70%, at least 75%, at least 80%, at least81%, at least 82%, at least 83%, at least 84%, at least 85%, at least86%, at least 87%, at least 88%, at least 89%, at least 90%, at least91%, at least 92%, at least 93%, at least 94%, at least 95%, at least96%, at least 97%, at least 98%, at least 99%, or 100% sequence identityto the polypeptide coding sequence of SEQ ID NO: 73 or the cDNA sequencethereof, at least 94%, at least 95%, at least 96%, at least 97%, atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 77 or the cDNA sequence thereof, or atleast 98%, at least 99%, or 100% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 75 or the cDNA sequence thereof.

[33] The polypeptide of any of paragraphs 29-32, comprising orconsisting of SEQ ID NO: 74, SEQ ID NO: 76, or SEQ ID NO: 78 or thepolypeptide of SEQ ID NO: 74, SEQ ID NO: 76, or SEQ ID NO: 78.

[34] The polypeptide of paragraph 29, which is a variant comprising thepolypeptide of SEQ ID NO: 74, SEQ ID NO: 76, or SEQ ID NO: 78 comprisinga substitution, deletion, and/or insertion at one or more positions.

[35] The polypeptide of paragraph 29, which is a fragment of SEQ ID NO:74, SEQ ID NO: 76, or SEQ ID NO: 78, wherein the fragment has xylanaseactivity.

[36] A composition comprising the polypeptide of any of paragraphs 1-35.

[37] An isolated polynucleotide encoding the polypeptide of any ofparagraphs 1-35.

[38] A nucleic acid construct or expression vector comprising thepolynucleotide of paragraph 37 operably linked to one or more controlsequences that direct the production of the polypeptide in an expressionhost.

[39] A recombinant host cell comprising the polynucleotide of paragraph37 operably linked to one or more control sequences that direct theproduction of the polypeptide.

[40] A method of producing the polypeptide of any of paragraphs 1-35,comprising: (a) cultivating a cell, which in its wild-type form producesthe polypeptide, under conditions conducive for production of thepolypeptide; and (b) recovering the polypeptide.

[41] A method of producing a polypeptide having enzyme activity,comprising: (a) cultivating the host cell of paragraph 39 underconditions conducive for production of the polypeptide; and (b)recovering the polypeptide.

[42] A transgenic plant, plant part or plant cell transformed with apolynucleotide encoding the polypeptide of any of paragraphs 1-35.

[43] A method of producing a polypeptide having xylanase activity,comprising: (a) cultivating the transgenic plant or plant cell ofparagraph 42 under conditions conducive for production of thepolypeptide; and (b) recovering the polypeptide.

[44] A method of producing a mutant of a parent cell, comprisinginactivating a polynucleotide encoding the polypeptide of any ofparagraphs 1-35, which results in the mutant producing less of thepolypeptide than the parent cell.

[45] A mutant cell produced by the method of paragraph 44. [46] Themutant cell of paragraph 45, further comprising a gene encoding a nativeor heterologous protein.

[47] A method of producing a protein, comprising: (a) cultivating themutant cell of paragraph 45 or 46 under conditions conducive forproduction of the protein; and (b) recovering the protein.

[48] A double-stranded inhibitory RNA (dsRNA) molecule comprising asubsequence of the polynucleotide of paragraph 37, wherein optionallythe dsRNA is an siRNA or an miRNA molecule.

[49] The double-stranded inhibitory RNA (dsRNA) molecule of paragraph48, which is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or moreduplex nucleotides in length.

[50] A method of inhibiting the expression of a polypeptide havingxylanase activity in a cell, comprising administering to the cell orexpressing in the cell the double-stranded inhibitory RNA (dsRNA)molecule of paragraph 48 or 49.

[51] A cell produced by the method of paragraph 50.

[52] The cell of paragraph 51, further comprising a gene encoding anative or heterologous protein.

[53] A method of producing a protein, comprising: (a) cultivating thecell of paragraph 51 or 52 under conditions conducive for production ofthe protein; and (b) recovering the protein.

[54] A process for degrading or converting a cellulosic orxylan-containing material, comprising: treating the cellulosic orxylan-containing material with an enzyme composition in the presence ofthe polypeptide having xylanase activity of any of paragraphs 1-35.

[55] The process of paragraph 54, wherein the cellulosic orxylan-containing material is pretreated.

[56] The process of paragraph 54 or 55, wherein the enzyme compositioncomprises one or more enzymes selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, an expansin, a laccase, a ligninolyticenzyme, a pectinase, a peroxidase, a protease, and a swollenin.

[57] The process of paragraph 56, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

[58] The process of paragraph 56, wherein the hemicellulase is one ormore enzymes selected from the group consisting of a xylanase, anacetylxylan esterase, a feruloyl esterase, an arabinofuranosidase, axylosidase, and a glucuronidase.

[59] The process of any of paragraphs 54-58, further comprisingrecovering the degraded cellulosic or xylan-containing material.

[60] The process of paragraph 59, wherein the degraded cellulosic orxylan-containing material is a sugar.

[61] The process of paragraph 60, wherein the sugar is selected from thegroup consisting of glucose, xylose, mannose, galactose, and arabinose.

[62] A process for producing a fermentation product, comprising: (a)saccharifying a cellulosic or xylan-containing material with an enzymecomposition in the presence of the polypeptide having xylanase activityof any of paragraphs 1-35; (b) fermenting the saccharified cellulosic orxylan-containing material with one or more fermenting microorganisms toproduce the fermentation product; and (c) recovering the fermentationproduct from the fermentation.

[63] The process of paragraph 62, wherein the cellulosic orxylan-containing material is pretreated.

[64] The process of paragraph 62 or 63, wherein the enzyme compositioncomprises one or more enzymes selected from the group consisting of acellulase, a polypeptide having cellulolytic enhancing activity, ahemicellulase, an esterase, an expansin, a laccase, a ligninolyticenzyme, a pectinase, a peroxidase, a protease, and a swollenin.

[65] The process of paragraph 64, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

[66] The process of paragraph 64, wherein the hemicellulase is one ormore enzymes selected from the group consisting of a xylanase, anacetylxylan esterase, a feruloyl esterase, an arabinofuranosidase, axylosidase, and a glucuronidase.

[67] The process of any of paragraphs 62-66, wherein steps (a) and (b)are performed simultaneously in a simultaneous saccharification andfermentation.

[68] The process of any of paragraphs 62-67, wherein the fermentationproduct is an alcohol, an alkane, a cycloalkane, an alkene, an aminoacid, a gas, isoprene, a ketone, an organic acid, or polyketide.

[69] A process of fermenting a cellulosic or xylan-containing material,comprising: fermenting the cellulosic or xylan-containing material withone or more fermenting microorganisms, wherein the cellulosic orxylan-containing material is saccharified with an enzyme composition inthe presence of the polypeptide having xylanase activity of any ofparagraphs 1-35.

[70] The process of paragraph 69, wherein the fermenting of thecellulosic or xylan-containing material produces a fermentation product.

[71] The process of paragraph 70, further comprising recovering thefermentation product from the fermentation.

[72] The process of paragraph 71, wherein the fermentation product is analcohol, an alkane, a cycloalkane, an alkene, an amino acid, a gas,isoprene, a ketone, an organic acid, or polyketide.

[73] The process of any of paragraphs 69-72, wherein the cellulosic orxylan-containing material is pretreated before saccharification.

[74] The process of any of paragraphs 69-73, wherein the enzymecomposition comprises one or more enzymes selected from the groupconsisting of a cellulase, a polypeptide having cellulolytic enhancingactivity, a hemicellulase, an esterase, an expansin, a laccase, aligninolytic enzyme, a pectinase, a peroxidase, a protease, and aswollenin.

[75] The process of paragraph 74, wherein the cellulase is one or moreenzymes selected from the group consisting of an endoglucanase, acellobiohydrolase, and a beta-glucosidase.

[76] The process of paragraph 74, wherein the hemicellulase is one ormore enzymes selected from the group consisting of a xylanase, anacetylxylan esterase, a feruloyl esterase, an arabinofuranosidase, axylosidase, and a glucuronidase.

[77] A whole broth formulation or cell culture composition comprisingthe polypeptide of any of paragraphs 1-35.

The invention described and claimed herein is not to be limited in scopeby the specific aspects herein disclosed, since these aspects areintended as illustrations of several aspects of the invention. Anyequivalent aspects are intended to be within the scope of thisinvention. Indeed, various modifications of the invention in addition tothose shown and described herein will become apparent to those skilledin the art from the foregoing description. Such modifications are alsointended to fall within the scope of the appended claims. In the case ofconflict, the present disclosure including definitions will control.

The invention claimed is:
 1. A nucleic acid construct comprising apolynucleotide encoding a polypeptide having cellobiohydrolase activity,wherein the polynucleotide is operably linked to one or moreheterologous control sequences that direct the production of thepolypeptide having cellobiohydrolase activity in a host cell, andwherein the polypeptide having cellobiohydrolase activity is selectedfrom the group consisting of: (a) a polypeptide having at least 90%sequence identity to the polypeptide of SEQ ID NO: 16; (b) a polypeptideencoded by a polynucleotide that hybridizes under very high stringencyconditions with the full-length complement SEQ ID NO: 15; or the cDNAsequence thereof; wherein very high stringency conditions are defined asprehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide,and washing three times each for 15 minutes using 2×SSC, 0.2% SDS at 70°C.; (c) a polypeptide encoded by a polynucleotide having at least 90%sequence identity to the polypeptide coding sequence of SEQ ID NO: 15;or the cDNA sequence thereof; (d) a fragment of the polypeptide of (a),(b), or (c) that has cellobiohydrolase activity; (e) a polypeptidecomprising SEQ ID NO: 16; and (f) a polypeptide encoded by thepolynucleotide of SEQ ID NO: 15; or the cDNA sequence thereof.
 2. Arecombinant host cell comprising the nucleic acid construct of claim 1.3. A method of producing a polypeptide having cellobiohydrolaseactivity, comprising: (a) cultivating the host cell of claim 2 underconditions conducive for production of the polypeptide; and (b)recovering the polypeptide.
 4. An isolated recombinant host cellcomprising a nucleic acid construct comprising a polynucleotide encodinga polypeptide having cellobiohydrolase activity, wherein thepolynucleotide is operably linked to one or more control sequences thatdirect the production of the polypeptide having cellobiohydrolaseactivity in a host cell, wherein the polypeptide havingcellobiohydrolase activity is heterologous to the host cell, and whereinthe polypeptide having cellobiohydrolase activity is selected from thegroup consisting of: (a) a polypeptide having at least 90% sequenceidentity to the polypeptide of SEQ ID NO: 16; (b) a polypeptide encodedby a polynucleotide that hybridizes under very high stringencyconditions with the full-length complement SEQ ID NO: 15; or the cDNAsequence thereof; wherein very high stringency conditions are defined asprehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide,and washing three times each for 15 minutes using 2×SSC, 0.2% SDS at 70°C.; (c) a polypeptide encoded by a polynucleotide having at least 90%sequence identity to the polypeptide coding sequence of SEQ ID NO: 15;or the cDNA sequence thereof; (d) a fragment of the polypeptide of (a),(b), or (c) that has cellobiohydrolase activity; (e) a polypeptidecomprising SEQ ID NO: 16; and (f) a polypeptide encoded by thepolynucleotide of SEQ ID NO: 15; or the cDNA sequence thereof.
 5. Amethod of producing a polypeptide having cellobiohydrolase activity,comprising: (a) cultivating the host cell of claim 4 under conditionsconducive for production of the polypeptide; and (b) recovering thepolypeptide.
 6. A process for degrading or converting a cellulosic orxylan-containing material, comprising: (a) treating the cellulosic orxylan-containing material with an enzyme composition comprising apolypeptide having cellobiohydrolase activity at a temperature of about50° C. to about 80° C., wherein the polypeptide having cellobiohydrolaseactivity is selected from the group consisting of: (1) a polypeptidehaving at least 90% sequence identity to the polypeptide of SEQ ID NO:16; (2) a polypeptide encoded by a polynucleotide that hybridizes undervery high stringency conditions with the full-length complement SEQ IDNO: 15; or the cDNA sequence thereof; wherein very high stringencyconditions are defined as prehybridization and hybridization at 42° C.in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmonsperm DNA, and 50% formamide, and washing three times each for 15minutes using 2×SSC, 0.2% SDS at 70° C.; (3) a polypeptide encoded by apolynucleotide having at least 90% sequence identity to the polypeptidecoding sequence of SEQ ID NO: 15; or the cDNA sequence thereof; (4) afragment of the polypeptide of (1), (2), or (3) that hascellobiohydrolase activity; (5) a polypeptide comprising SEQ ID NO: 16;and (6) a polypeptide encoded by the polynucleotide of SEQ ID NO: 15; orthe cDNA sequence thereof.
 7. The process of claim 6, further comprisingrecovering the degraded or converted cellulosic or xylan-containingmaterial.
 8. The process of claim 6, wherein the cellulosic orxylan-containing material is pretreated.
 9. The process of claim 6,wherein the degraded or converted cellulosic or xylan-containingmaterial is a sugar.
 10. The process of claim 9, wherein the sugar isselected from the group consisting of glucose, xylose, mannose,galactose, and arabinose.
 11. The process of claim 6, wherein the enzymecomposition further comprises one or more enzymes selected from thegroup consisting of a cellulase, a polypeptide having cellobiohydrolaseactivity, a hemicellulase, an esterase, an expansin, a laccase, aligninolytic enzyme, a pectinase, a peroxidase, a protease, and aswollenin.
 12. A process for producing a fermentation product,comprising: (a) saccharifying a cellulosic or xylan-containing materialwith an enzyme composition comprising a polypeptide havingcellobiohydrolase activity at a temperature of about 50° C. to about 80°C., wherein the polypeptide having cellobiohydrolase activity isselected from the group consisting of: (1) a polypeptide having at least90% sequence identity to the polypeptide of SEQ ID NO: 16; (2) apolypeptide encoded by a polynucleotide that hybridizes under very highstringency conditions with the full-length complement SEQ ID NO: 15; orthe cDNA sequence thereof; wherein very high stringency conditions aredefined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3%SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 50%formamide, and washing three times each for 15 minutes using 2×SSC, 0.2%SDS at 70° C.; (3) a polypeptide encoded by a polynucleotide having atleast 90% sequence identity to the polypeptide coding sequence of SEQ IDNO: 15; or the cDNA sequence thereof; (4) a fragment of the polypeptideof (1), (2), or (3) that has cellobiohydrolase activity; (5) apolypeptide comprising SEQ ID NO: 16; and (6) a polypeptide encoded bythe polynucleotide of SEQ ID NO: 15; or the cDNA sequence thereof (b)fermenting the saccharified cellulosic or xylan-containing material withone or more fermenting microorganisms to produce the fermentationproduct; and (c) recovering the fermentation product from thefermentation.
 13. The process of claim 12, wherein the cellulosic orxylan-containing material is pretreated.
 14. The process of claim 12,wherein the enzyme composition further comprises one or more enzymesselected from the group consisting of a cellulase, a polypeptide havingcellobiohydrolase activity, a hemicellulase, an esterase, an expansin, alaccase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease,and a swollenin.
 15. The process of claim 12, wherein steps (a) and (b)are performed simultaneously in a simultaneous saccharification andfermentation.
 16. A process of fermenting a cellulosic orxylan-containing material, comprising: fermenting the cellulosic orxylan-containing material with one or more fermenting microorganisms,wherein the cellulosic or xylan-containing material is saccharified withan enzyme composition comprising a polypeptide having cellobiohydrolaseactivity at a temperature of about 50° C. to about 80° C., wherein thepolypeptide having cellobiohydrolase activity is selected from the groupconsisting of: (1) a polypeptide having at least 90% sequence identityto the polypeptide of SEQ ID NO: 16; (2) a polypeptide encoded by apolynucleotide that hybridizes under very high stringency conditionswith the full-length complement SEQ ID NO: 15; or the cDNA sequencethereof; wherein very high stringency conditions are defined asprehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide,and washing three times each for 15 minutes using 2×SSC, 0.2% SDS at 70°C.; (3) a polypeptide encoded by a polynucleotide having at least 90%sequence identity to the polypeptide coding sequence of SEQ ID NO: 15,or the cDNA sequence thereof; (4) a fragment of the polypeptide of (1),(2), or (3) that has cellobiohydrolase activity; (5) a polypeptidecomprising SEQ ID NO: 48, SEQ ID NO: 50, SEQ ID NO: 56; or SEQ ID NO:79; and (6) a polypeptide encoded by the polynucleotide of SEQ ID NO:15; or the cDNA sequence thereof.
 17. The process of claim 16, whereinthe cellulosic or xylan-containing material is pretreated.
 18. Theprocess of claim 16, wherein the fermenting of the cellulosic orxylan-containing material produces a fermentation product.
 19. Theprocess of claim 18, further comprising recovering the fermentationproduct from the fermentation.
 20. The process of claim 16, wherein theenzyme composition further comprises one or more enzymes selected fromthe group consisting of a cellulase, a polypeptide havingcellobiohydrolase activity, a hemicellulase, an esterase, an expansin, alaccase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease,and a swollenin.